add Lee-Ping's MTSVVVR custom integrator

2igd/2igd.md1.log

@@ -0,0 +1,12 @@
+Command line:
+	/home/case/mm/OMM_Amoeba_Scripts/runmd.py --xml system.xml -p 2igd_solvated.pdb -x 2igd.md1.nc -r 2igd.md1.x -o 2igd.md1.o -s 2igd.md0.x -n 10000 --interval 500 --gamma_ln 5.0
+Parsing XML file system.xml
+No Andersen thermostat found in the system.xml file
+Parsing PDB file 2igd_solvated.pdb
+Langevin:   300.00K,     5.00 ps-1,     1.00 fs
+Setting coordinates and velocities from restart file 2igd.md0.x
+Running the simulation for 10000 steps!
+/home/case/amber20/lib/python3.7/site-packages/parmed/amber/netcdffiles.py:409: UserWarning: Could not find netCDF4 module. Falling back on scipy implementation, which can significantly slow down simulations if used as a reporter
+  warnings.warn('Could not find netCDF4 module. Falling back on '
+/home/case/amber20/lib/python3.7/site-packages/parmed/amber/netcdffiles.py:83: UserWarning: Could not find netCDF4 module. Falling back on scipy implementation, which can significantly slow down simulations if used as a reporter
+  warnings.warn('Could not find netCDF4 module. Falling back on '

2igd/2igd.md1.o

@@ -0,0 +1,21 @@
+#"Step"	"Time (ps)"	"Potential Energy (kilocalorie/mole)"	"Kinetic Energy (kilocalorie/mole)"	"Total Energy (kilocalorie/mole)"	"Temperature (K)"	"Box Volume (angstrom**3)"	"Density (gram/(item*milliliter))"
+500	0.5000000000000003	-67126.62813673605	17112.137867719848	-50014.4902690162	271.0594403356015	241303.376270884	0.8893032985584709
+1000	1.0000000000000007	-64609.330052802565	18654.810355873757	-45954.51969692881	295.49565891288006	241303.376270884	0.8893032985584709
+1500	1.4999999999999456	-63931.662059840186	18923.161085430293	-45008.50097440989	299.7463842827626	241303.376270884	0.8893032985584709
+2000	1.9999999999998905	-63893.71771925281	18948.571777238605	-44945.145942014206	300.1488943579704	241303.376270884	0.8893032985584709
+2500	2.4999999999998357	-64087.33350421746	18692.81164114936	-45394.52186306809	296.0976063257904	241303.376270884	0.8893032985584709
+3000	2.9999999999997806	-64287.91915871105	18936.713735852634	-45351.20542285841	299.9610607812189	241303.376270884	0.8893032985584709
+3500	3.4999999999997256	-64182.066665769016	18920.291619915053	-45261.77504585396	299.70093141634493	241303.376270884	0.8893032985584709
+4000	3.9999999999996705	-64164.11283980876	19107.2301592744	-45056.88268053436	302.6620725810316	241303.376270884	0.8893032985584709
+4500	4.4999999999998375	-63962.70075510813	19114.15589751095	-44848.54485759718	302.7717775603172	241303.376270884	0.8893032985584709
+5000	5.000000000000004	-64138.226023869	18864.969824833202	-45273.25619903579	298.82462391291284	241303.376270884	0.8893032985584709
+5500	5.500000000000171	-64283.491412792646	18895.995820142256	-45387.49559265038	299.3160814379361	241303.376270884	0.8893032985584709
+6000	6.000000000000338	-64252.679657317036	18887.874342575677	-45364.80531474136	299.18743572569883	241303.376270884	0.8893032985584709
+6500	6.500000000000505	-64430.169135497934	18944.664401188777	-45485.504734309165	300.08700079601834	241303.376270884	0.8893032985584709
+7000	7.000000000000672	-64818.93997722294	18832.500698698987	-45986.43927852395	298.31030692773186	241303.376270884	0.8893032985584709
+7500	7.500000000000839	-64945.7266958398	18862.10107277413	-46083.62562306567	298.7791823477732	241303.376270884	0.8893032985584709
+8000	8.000000000001005	-64951.74541808399	19122.839296731327	-45828.90612135266	302.9093242158596	241303.376270884	0.8893032985584709
+8500	8.500000000000728	-64983.18854892212	18947.16058908567	-46036.02795983645	300.1265408756703	241303.376270884	0.8893032985584709
+9000	9.000000000000451	-64927.125931312556	19004.029284111646	-45923.09664720091	301.027351561367	241303.376270884	0.8893032985584709
+9500	9.500000000000174	-64864.14757958011	18951.48669350685	-45912.66088607327	300.1950671727527	241303.376270884	0.8893032985584709
+10000	9.999999999999897	-64799.1494117838	19015.8007725657	-45783.3486392181	301.2138141236101	241303.376270884	0.8893032985584709

2igd/2igd.md1.o.info

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+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
+
+  On step 10000 of 10000
+
+  Total Energy     =  -45783.3486
+  Potential Energy =  -64799.1494
+  Kinetic Energy   =   19015.8008
+
+ Time for last      500 steps:    23.7705 s. (1.817 ns/day)
+ Time for all     10000 steps:   472.5922 s. (1.828 ns/day)
+
+ Estimated time to completion: 0.000 sec.
+
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

2igd/SimulatePDB.py

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+from openmm.app import *
+from openmm import *
+from openmm.unit import *
+from sys import stdout
+import parmed as pmd
+u = pmd.unit
+
+pdb = PDBFile('2igd_solvated.pdb')
+forcefield = ForceField('../amoeba2018.xml')
+system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME,
+        nonbondedCutoff=1*nanometer, constraints=HBonds)
+integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
+simulation = Simulation(pdb.topology, system, integrator)
+simulation.context.setPositions(pdb.positions)
+
+e=simulation.context.getState(getEnergy=True).getPotentialEnergy()
+print(' Initial energy = %10.4f kcal/mol' % e.value_in_unit(u.kilocalories_per_mole))
+
+# Now write a serialized state that has coordinates
+print('Serializing the System...')
+with open('system2.xml', 'w') as f:
+    f.write(openmm.XmlSerializer.serialize(system))
+print('Writing serialized XML restart file...')
+with open('restart.xml', 'w') as f:
+    f.write(
+            openmm.XmlSerializer.serialize(
+                simulation.context.getState(
+                    getPositions=True, getVelocities=True, getForces=True,
+                    enforcePeriodicBox=system.usesPeriodicBoundaryConditions(),
+                    getEnergy=True
+                )
+            )
+    )
+
+print('Done!')
+quit()
+
+simulation.minimizeEnergy()
+simulation.reporters.append(PDBReporter('output.pdb', 1000))
+simulation.reporters.append(StateDataReporter(stdout, 1000, step=True,
+        potentialEnergy=True, temperature=True))
+simulation.step(10000)