Re: "Jump" in Energy and Volume graphs of my MD

From: Daniela Rivas (dani.rivas.r_at_gmail.com)
Date: Wed Mar 30 2016 - 15:49:01 CDT

Yes, I'm very sure. I used this:

# INPUT FILES #

structure Modelo23_memb_ion.psf
coordinates Modelo23_memb_ion.pdb

# Continuing a job from the restart files #

if {1} {
set inputname dinamica_modelo.restart ;# only need to edit
this in one place!
binCoordinates $inputname.coor ;# coordinates from last run
(binary)
binVelocities $inputname.vel ;# velocities from last run
(binary)
extendedSystem $inputname.xsc ;# cell dimensions from last run
firsttimestep 28763000 ;# last step of
previous run
numsteps 100000000 ;# run stops when this step is
reached
}

# FORCE-FIELD PARAMETERS #

paraTypeCharmm on
parameters par_all27_prot_lipid.inp

exclude scaled1-4
1-4scaling 1.0
switching on
switchDist 8.5
cutoff 10
pairlistdist 11.5

# INTEGRATOR PARAMETERS #

timestep 1
stepsPerCycle 20
nonBondedFreq 2
fullElectFrequency 4

# FIXED ATOMS #

fixedAtoms on
fixedAtomsForces off
fixedAtomsFile myfixedatoms.pdb
fixedAtomsCol B

# CONSTRAINTS #

#constraints off
#consRef off
#consKFile off
#consKCol off

# PRESSURE AND TEMPERATURE CONTROL #

langevin on
langevinDamping 10
langevinTemp 310
langevinHydrogen no

langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 200
langevinPistonDecay 100
langevinPistonTemp 310

useGroupPressure yes # smaller fluctuations
useFlexibleCell yes # allow dimensions to fluctuate independently
useConstantRatio yes # fix shape in x-y plane

# OUTPUT FILES #

binaryoutput off
outputname dinamica_modelo2
outputEnergies 500
outputTiming 500
restartfreq 1000000
xstFreq 500
dcdFreq 500
wrapAll on
wrapNearest on

# DYNAMICS #

run 100000000
output Modelo_final

On Wed, Mar 30, 2016 at 5:23 PM, Peter Freddolino <petefred_at_umich.edu>
wrote:

> Are you sure that on restart you are reading the extended system
> information from the restart file and not resetting the cell basis vectors?
> Best,
> Peter
>
> > On Mar 30, 2016, at 4:04 PM, Daniela Rivas <dani.rivas.r_at_gmail.com>
> wrote:
> >
> > Dear NAMD users,
> >
> > When analyzing the basic data (T, P, V, Energy and protein RMSD) of my
> MD I found that there was a "jump" in my Volume and Potential Energy
> graphs. This jump occurs just when I had to stop the simulation and
> re-started it from the restart files from the last step. I used all the
> restart files to re-start my simulation, and there's no problem with the
> Temperature, Pressure, Kinetic Energy or protein RMSD. Any thoughts of what
> could have happened? Has anyone else had this problem when restarting a MD?
> >
> > I hope you can help me solve this riddle. Thanks in advance!
>
>

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