Updated demos

.devcontainer/Dockerfile

@@ -1,5 +1,7 @@
 FROM ghcr.io/becksteinlab/streaming-md-docker:main-common-cpu
 
+FROM ghcr.io/becksteinlab/streaming-namd-docker:main-common-gpu
+
 COPY env.yaml env.yaml
 RUN . /opt/conda/etc/profile.d/conda.sh && \
         conda env create -n workshop --file=env.yaml

gromacs-demos/msd/demo.py

@@ -0,0 +1,40 @@
+from imdclient.IMDREADER import IMDReader
+import numpy as np
+import MDAnalysis as mda
+import logging
+import dynplot as dyn
+import vdos as vd
+import time as t
+
+# %%
+logger = logging.getLogger("imdclient.IMDClient")
+file_handler = logging.FileHandler("imdreader.log")
+formatter = logging.Formatter(
+    "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
+)
+file_handler.setFormatter(formatter)
+logger.addHandler(file_handler)
+logger.setLevel(logging.INFO)
+
+# %%
+u = mda.Universe("mda.tpr", "imd://localhost:8888",buffersize = 10*1024*1024)
+sel = u.select_atoms("resname SOL")
+vdos = vd.vdos(sel,200)
+
+vd.vdosLib.omp_set_num_threads(2)
+tStep = 0
+for ts in u.trajectory:
+    vdos.single_frame(tStep,ts.time)
+    if tStep == 0:
+        d = dyn.dynamicPlot([0,1000],"wavenumber (cm^-1)",[0,12000],"VDoS (arb. u.)","")
+    elif tStep % 200 == 0:
+        vdos.copyResidueList()
+        vdos.postProcess(vdos.residueListCopy,mode = "total+single")
+        total = np.array(vdos.totVDoS[0])
+        single = np.array(vdos.totVDoS[1])
+        d.update(vdos.wavenumber, total, single)
+    tStep += 1
+# %%
+logger.info(f"Parsed {tStep} frames")
+
+

gromacs-demos/msd/dynplot.py

@@ -0,0 +1,35 @@
+import matplotlib.pyplot as plt
+import seaborn as sns
+sns.set_theme()
+plt.ion()
+
+class dynamicPlot:
+    def __init__(self,xRange,xLabel,yRange,yLabel,title):
+        self.xRange = xRange
+        self.xLabel = xLabel
+        self.yRange = yRange
+        self.yLabel = yLabel
+        self.title = title
+        self.prepare()
+
+    def prepare(self):
+        #Set up plot
+        self.figure, self.ax = plt.subplots()
+        self.l1, = self.ax.plot([],[], color = "red", linewidth = 2.0, label = "total")
+        self.l2, = self.ax.plot([],[], color = "blue", linewidth = 2.0, label = "single molecule")
+        self.ax.set_xlim(self.xRange[0], self.xRange[1])
+        self.ax.set_ylim(self.yRange[0], self.yRange[1])
+        self.ax.set_xlabel(self.xLabel)
+        self.ax.set_ylabel(self.yLabel)
+        self.ax.set_title(self.title)
+        self.ax.legend()
+
+    def update(self, xData, yData1, yData2):
+        #Update data (with the new _and_ the old points)
+        self.l1.set_xdata(xData)
+        self.l1.set_ydata(yData1)
+        self.l2.set_xdata(xData)
+        self.l2.set_ydata(yData2)
+        #We need to draw *and* flush
+        self.figure.canvas.draw()
+        self.figure.canvas.flush_events()

gromacs-demos/msd/imd.mdp

@@ -0,0 +1,57 @@
+title                   = PRODUCTION IN NPT
+; Run parameters
+integrator              = md        ; leap-frog integrator
+nsteps                  = 25000     ; 1 * 25000 = 25 ps
+dt                      = 0.001     ; 1 fs
+; Output control
+nstxout                 = 5000      ; save coordinates every 5 ps
+nstvout                 = 5000      ; save velocities every 5 ps
+nstenergy               = 5000      ; save energies every 5 ps
+nstlog                  = 5000      ; update log file every 5 ps
+; Center of mass (COM) motion
+nstcomm                 = 10        ; remove COM motion every 10 steps
+comm-mode               = Linear    ; remove only COM translation (liquids in PBC) 
+; Bond parameters
+continuation            = yes       ; first dynamics run
+constraint_algorithm    = lincs     ; holonomic constraints
+constraints             = all-bonds ; all bonds lengths are constrained
+lincs_iter              = 1         ; accuracy of LINCS
+lincs_order             = 4         ; also related to accuracy
+; Nonbonded settings
+cutoff-scheme           = Verlet    ; Buffered neighbor searching
+ns_type                 = grid      ; search neighboring grid cells
+nstlist                 = 10        ; 10 fs, largely irrelevant with Verlet
+rcoulomb                = 1.0       ; short-range electrostatic cutoff (in nm)
+rvdw                    = 1.0       ; short-range van der Waals cutoff (in nm)
+DispCorr                = EnerPres  ; account for cut-off vdW scheme
+; Electrostatics
+coulombtype             = PME       ; Particle Mesh Ewald for long-range electrostatics
+pme_order               = 4         ; cubic interpolation
+fourierspacing          = 0.12      ; grid spacing for FFT
+; Temperature coupling is on
+tcoupl                  = Nose-Hoover       ; good for production, after equilibration
+; we define separate thermostats for the solute and solvent (need to adapt)
+; see default groups defined by Gromacs for your system or define your own (make_ndx)
+tc-grps                 = Protein  non-Protein  ; the separate groups for the thermostats
+tau-t                   = 1.0      1.0      ; time constants for thermostats (ps)
+ref-t                   = 300      300      ; reference temperature for thermostats (K)
+; Pressure coupling is off
+pcoupl                  = Parrinello-Rahman ; good for production, after equilibration
+tau-p                   = 2.0               ; time constant for barostat (ps)
+compressibility         = 4.5e-5            ; compressibility (1/bar) set to water at ~300K
+ref-p                   = 1.0               ; reference pressure for barostat (bar)
+; Periodic boundary conditions
+pbc                     = xyz       ; 3-D PBC
+; Velocity generation
+gen_vel                 = no
+; IMD group
+IMD-group               = System
+IMD-version             = 3
+IMD-nst                 = 5
+IMD-time                = yes
+IMD-box                 = yes
+IMD-coords              = yes
+IMD-unwrap              = yes
+IMD-forces              = no
+IMD-vels                = yes
+IMD-energies            = no

gromacs-demos/msd/imdreader.log

@@ -0,0 +1,139 @@
+2024-11-14 11:29:27,762 - imdclient.IMDClient - INFO - Parsed 63 frames
+2024-11-14 11:31:10,543 - imdclient.IMDClient - INFO - Parsed 200 frames
+2024-11-14 11:56:53,090 - imdclient.IMDClient - INFO - Parsed 1032 frames
+2024-11-14 11:56:53,090 - imdclient.IMDClient - INFO - Parsed 1032 frames
+2024-11-14 11:56:53,090 - imdclient.IMDClient - INFO - Parsed 1032 frames
+2024-11-14 12:14:45,608 - imdclient.IMDClient - INFO - Parsed 3126 frames
+2024-11-15 11:26:42,832 - imdclient.IMDClient - INFO - Parsed 242 frames
+2024-11-15 11:29:59,980 - imdclient.IMDClient - INFO - Parsed 368 frames
+2024-11-15 11:29:59,980 - imdclient.IMDClient - INFO - Parsed 368 frames
+2024-11-19 11:40:03,661 - imdclient.IMDClient - INFO - Parsed 3126 frames
+2024-11-20 11:23:33,248 - imdclient.IMDClient - INFO - Parsed 658 frames
+2024-11-20 17:47:37,419 - imdclient.IMDClient - INFO - Parsed 950 frames
+2024-11-20 17:49:17,983 - imdclient.IMDClient - INFO - Parsed 9 frames
+2024-11-20 17:49:17,983 - imdclient.IMDClient - INFO - Parsed 9 frames
+2024-11-20 17:50:29,314 - imdclient.IMDClient - INFO - Parsed 487 frames
+2024-11-20 17:50:29,314 - imdclient.IMDClient - INFO - Parsed 487 frames
+2024-11-20 17:50:29,314 - imdclient.IMDClient - INFO - Parsed 487 frames
+2024-11-20 17:51:10,677 - imdclient.IMDClient - INFO - Parsed 287 frames
+2024-11-20 17:51:10,677 - imdclient.IMDClient - INFO - Parsed 287 frames
+2024-11-20 17:51:10,677 - imdclient.IMDClient - INFO - Parsed 287 frames
+2024-11-20 17:51:10,677 - imdclient.IMDClient - INFO - Parsed 287 frames
+2024-11-20 17:51:47,083 - imdclient.IMDClient - INFO - Parsed 259 frames
+2024-11-20 17:51:47,083 - imdclient.IMDClient - INFO - Parsed 259 frames
+2024-11-20 17:51:47,083 - imdclient.IMDClient - INFO - Parsed 259 frames
+2024-11-20 17:51:47,083 - imdclient.IMDClient - INFO - Parsed 259 frames
+2024-11-20 17:51:47,083 - imdclient.IMDClient - INFO - Parsed 259 frames
+2024-11-20 17:58:52,086 - imdclient.IMDClient - INFO - Parsed 118 frames
+2024-11-20 18:00:27,665 - imdclient.IMDClient - INFO - Parsed 255 frames
+2024-11-20 18:00:27,665 - imdclient.IMDClient - INFO - Parsed 255 frames
+2024-11-20 18:09:20,440 - imdclient.IMDClient - INFO - Parsed 1 frames
+2024-11-20 18:09:47,407 - imdclient.IMDClient - INFO - Parsed 3 frames
+2024-11-20 18:09:47,407 - imdclient.IMDClient - INFO - Parsed 3 frames
+2024-11-20 18:39:34,249 - imdclient.IMDClient - INFO - Parsed 138 frames
+2024-11-20 18:41:00,368 - imdclient.IMDClient - INFO - Parsed 309 frames
+2024-11-20 18:41:00,368 - imdclient.IMDClient - INFO - Parsed 309 frames
+2024-11-20 18:41:53,435 - imdclient.IMDClient - INFO - Parsed 178 frames
+2024-11-20 18:41:53,435 - imdclient.IMDClient - INFO - Parsed 178 frames
+2024-11-20 18:41:53,435 - imdclient.IMDClient - INFO - Parsed 178 frames
+2024-11-20 18:43:04,857 - imdclient.IMDClient - INFO - Parsed 208 frames
+2024-11-20 18:43:04,857 - imdclient.IMDClient - INFO - Parsed 208 frames
+2024-11-20 18:43:04,857 - imdclient.IMDClient - INFO - Parsed 208 frames
+2024-11-20 18:43:04,857 - imdclient.IMDClient - INFO - Parsed 208 frames
+2024-11-20 18:54:00,943 - imdclient.IMDClient - INFO - Parsed 778 frames
+2024-11-20 18:56:25,123 - imdclient.IMDClient - INFO - Parsed 373 frames
+2024-11-20 18:56:25,123 - imdclient.IMDClient - INFO - Parsed 373 frames
+2024-11-20 18:57:46,316 - imdclient.IMDClient - INFO - Parsed 26 frames
+2024-11-20 18:57:46,316 - imdclient.IMDClient - INFO - Parsed 26 frames
+2024-11-20 18:57:46,316 - imdclient.IMDClient - INFO - Parsed 26 frames
+2024-11-20 18:58:58,910 - imdclient.IMDClient - INFO - Parsed 247 frames
+2024-11-20 18:58:58,910 - imdclient.IMDClient - INFO - Parsed 247 frames
+2024-11-20 18:58:58,910 - imdclient.IMDClient - INFO - Parsed 247 frames
+2024-11-20 18:58:58,910 - imdclient.IMDClient - INFO - Parsed 247 frames
+2024-11-20 19:10:17,605 - imdclient.IMDClient - INFO - Parsed 3126 frames
+2024-11-20 19:10:17,605 - imdclient.IMDClient - INFO - Parsed 3126 frames
+2024-11-20 19:10:17,605 - imdclient.IMDClient - INFO - Parsed 3126 frames
+2024-11-20 19:10:17,605 - imdclient.IMDClient - INFO - Parsed 3126 frames
+2024-11-20 19:10:17,605 - imdclient.IMDClient - INFO - Parsed 3126 frames
+2024-11-20 19:11:29,729 - imdclient.IMDClient - INFO - Parsed 44 frames
+2024-11-20 19:11:29,729 - imdclient.IMDClient - INFO - Parsed 44 frames
+2024-11-20 19:11:29,729 - imdclient.IMDClient - INFO - Parsed 44 frames
+2024-11-20 19:11:29,729 - imdclient.IMDClient - INFO - Parsed 44 frames
+2024-11-20 19:11:29,729 - imdclient.IMDClient - INFO - Parsed 44 frames
+2024-11-20 19:11:29,729 - imdclient.IMDClient - INFO - Parsed 44 frames
+2024-11-20 19:20:41,617 - imdclient.IMDClient - INFO - Parsed 3082 frames
+2024-11-20 19:20:41,617 - imdclient.IMDClient - INFO - Parsed 3082 frames
+2024-11-20 19:20:41,617 - imdclient.IMDClient - INFO - Parsed 3082 frames
+2024-11-20 19:20:41,617 - imdclient.IMDClient - INFO - Parsed 3082 frames
+2024-11-20 19:20:41,617 - imdclient.IMDClient - INFO - Parsed 3082 frames
+2024-11-20 19:20:41,617 - imdclient.IMDClient - INFO - Parsed 3082 frames
+2024-11-20 19:20:41,617 - imdclient.IMDClient - INFO - Parsed 3082 frames
+2024-11-20 20:14:15,389 - imdclient.IMDClient - INFO - Parsed 303 frames
+2024-11-20 20:14:15,389 - imdclient.IMDClient - INFO - Parsed 303 frames
+2024-11-20 20:14:15,389 - imdclient.IMDClient - INFO - Parsed 303 frames
+2024-11-20 20:14:15,389 - imdclient.IMDClient - INFO - Parsed 303 frames
+2024-11-20 20:14:15,389 - imdclient.IMDClient - INFO - Parsed 303 frames
+2024-11-20 20:20:25,324 - imdclient.IMDClient - INFO - Parsed 337 frames
+2024-11-20 20:23:04,235 - imdclient.IMDClient - INFO - Parsed 105 frames
+2024-11-20 20:23:04,235 - imdclient.IMDClient - INFO - Parsed 105 frames
+2024-11-20 20:25:14,369 - imdclient.IMDClient - INFO - Parsed 106 frames
+2024-11-20 20:25:14,369 - imdclient.IMDClient - INFO - Parsed 106 frames
+2024-11-20 20:25:14,369 - imdclient.IMDClient - INFO - Parsed 106 frames
+2024-11-20 20:26:32,546 - imdclient.IMDClient - INFO - Parsed 76 frames
+2024-11-20 20:26:32,546 - imdclient.IMDClient - INFO - Parsed 76 frames
+2024-11-20 20:26:32,546 - imdclient.IMDClient - INFO - Parsed 76 frames
+2024-11-20 20:26:32,546 - imdclient.IMDClient - INFO - Parsed 76 frames
+2024-11-20 20:32:05,845 - imdclient.IMDClient - INFO - Parsed 608 frames
+2024-11-20 20:32:43,482 - imdclient.IMDClient - INFO - Parsed 455 frames
+2024-11-20 20:32:43,482 - imdclient.IMDClient - INFO - Parsed 455 frames
+2024-11-20 20:33:42,577 - imdclient.IMDClient - INFO - Parsed 446 frames
+2024-11-20 20:33:42,577 - imdclient.IMDClient - INFO - Parsed 446 frames
+2024-11-20 20:33:42,577 - imdclient.IMDClient - INFO - Parsed 446 frames
+2024-11-20 20:39:16,276 - imdclient.IMDClient - INFO - Parsed 522 frames
+2024-11-20 20:39:42,412 - imdclient.IMDClient - INFO - Parsed 260 frames
+2024-11-20 20:39:42,412 - imdclient.IMDClient - INFO - Parsed 260 frames
+2024-11-21 06:49:48,501 - imdclient.IMDClient - INFO - Parsed 1913 frames
+2024-11-21 06:55:35,490 - imdclient.IMDClient - INFO - Parsed 844 frames
+2024-11-21 06:56:13,066 - imdclient.IMDClient - INFO - Parsed 103 frames
+2024-11-21 06:56:13,066 - imdclient.IMDClient - INFO - Parsed 103 frames
+2024-11-21 06:57:09,594 - imdclient.IMDClient - INFO - Parsed 604 frames
+2024-11-21 06:57:09,594 - imdclient.IMDClient - INFO - Parsed 604 frames
+2024-11-21 06:57:09,594 - imdclient.IMDClient - INFO - Parsed 604 frames
+2024-11-21 06:57:09,594 - imdclient.IMDClient - INFO - Parsed 604 frames
+2024-11-21 07:13:06,546 - imdclient.IMDClient - INFO - Parsed 171 frames
+2024-11-21 07:13:06,546 - imdclient.IMDClient - INFO - Parsed 171 frames
+2024-11-21 07:13:06,546 - imdclient.IMDClient - INFO - Parsed 171 frames
+2024-11-21 07:13:06,546 - imdclient.IMDClient - INFO - Parsed 171 frames
+2024-11-21 07:13:06,546 - imdclient.IMDClient - INFO - Parsed 171 frames
+2024-11-21 07:32:22,935 - imdclient.IMDClient - INFO - Parsed 448 frames
+2024-11-21 07:32:22,935 - imdclient.IMDClient - INFO - Parsed 448 frames
+2024-11-21 07:32:22,935 - imdclient.IMDClient - INFO - Parsed 448 frames
+2024-11-21 07:32:22,935 - imdclient.IMDClient - INFO - Parsed 448 frames
+2024-11-21 07:32:22,935 - imdclient.IMDClient - INFO - Parsed 448 frames
+2024-11-21 07:32:22,935 - imdclient.IMDClient - INFO - Parsed 448 frames
+2024-11-21 07:43:08,295 - imdclient.IMDClient - INFO - Parsed 104 frames
+2024-11-21 07:43:08,295 - imdclient.IMDClient - INFO - Parsed 104 frames
+2024-11-21 07:43:08,295 - imdclient.IMDClient - INFO - Parsed 104 frames
+2024-11-21 07:43:08,295 - imdclient.IMDClient - INFO - Parsed 104 frames
+2024-11-21 07:43:08,295 - imdclient.IMDClient - INFO - Parsed 104 frames
+2024-11-21 07:43:08,295 - imdclient.IMDClient - INFO - Parsed 104 frames
+2024-11-21 07:43:08,295 - imdclient.IMDClient - INFO - Parsed 104 frames
+2024-11-21 07:43:41,155 - imdclient.IMDClient - INFO - Parsed 281 frames
+2024-11-21 07:43:41,155 - imdclient.IMDClient - INFO - Parsed 281 frames
+2024-11-21 07:43:41,155 - imdclient.IMDClient - INFO - Parsed 281 frames
+2024-11-21 07:43:41,155 - imdclient.IMDClient - INFO - Parsed 281 frames
+2024-11-21 07:43:41,155 - imdclient.IMDClient - INFO - Parsed 281 frames
+2024-11-21 07:43:41,155 - imdclient.IMDClient - INFO - Parsed 281 frames
+2024-11-21 07:43:41,155 - imdclient.IMDClient - INFO - Parsed 281 frames
+2024-11-21 07:43:41,155 - imdclient.IMDClient - INFO - Parsed 281 frames
+2024-11-21 08:08:23,598 - imdclient.IMDClient - INFO - Parsed 794 frames
+2024-11-21 08:08:23,598 - imdclient.IMDClient - INFO - Parsed 794 frames
+2024-11-21 08:08:23,598 - imdclient.IMDClient - INFO - Parsed 794 frames
+2024-11-21 08:08:23,598 - imdclient.IMDClient - INFO - Parsed 794 frames
+2024-11-21 08:08:23,598 - imdclient.IMDClient - INFO - Parsed 794 frames
+2024-11-21 08:08:23,598 - imdclient.IMDClient - INFO - Parsed 794 frames
+2024-11-21 08:08:23,598 - imdclient.IMDClient - INFO - Parsed 794 frames
+2024-11-21 08:08:23,598 - imdclient.IMDClient - INFO - Parsed 794 frames
+2024-11-21 08:08:23,598 - imdclient.IMDClient - INFO - Parsed 794 frames
+2024-11-21 08:23:24,180 - imdclient.IMDClient - INFO - Parsed 3126 frames
+2024-11-21 08:37:03,919 - imdclient.IMDClient - INFO - Parsed 3126 frames

gromacs-demos/msd/run.sh

@@ -0,0 +1,30 @@
+#!/bin/bash
+
+echo "setting GROMACS version"
+source /scratch/hcho96/Research/imd-v3/gromacs-imd-v3/bin/GMXRC
+
+#if [ ! -f libvdos.so ]; then
+#echo "compiling C libraries"
+#gcc -O3 -fopenmp -fpic -lgsl -lgslcblas -c vdos.c
+#gcc -L/home/hcho96/.conda/envs/imdreader-test/lib -I/home/hcho96/.conda/envs/imdreader-test/include -O3 -fopenmp -fpic -lgsl -lgslcblas -c vdos.c
+#gcc -shared -lgomp -lgsl -lgslcblas vdos.o -o libvdos.so
+#gcc -L/home/hcho96/.conda/envs/imdreader-test/lib -I/home/hcho96/.conda/envs/imdreader-test/include -shared -lgomp -lgsl -lgslcblas vdos.o -o libvdos.so
+#fi
+
+mkdir -p imd
+cd imd
+if [ ! -f topol.tpr ]; then
+echo "running grompp"
+gmx grompp -f ../imd.mdp -c ../start.gro -p ../topol.top -o >& grompp.out
+fi
+echo "starting mdrun"
+echo ""
+echo "**************************************************************"
+echo "wait a few seconds, then:"
+echo "run (in separate terminal): python demo.py"
+echo "**************************************************************"
+echo ""
+# modify gromacs execution string according to available resources
+# here we use 2 parallel threads
+gmx mdrun -v -nt 12 -imdwait -imdport 8891
+cd ..