From: Peter Freddolino (petefred_at_umich.edu)
Date: Wed Mar 30 2016 - 15:56:22 CDT
Hi Daniela,
How big is the jump that you see in potential energy and volume? (absolute and relative)
Could you provide a diff between the config file below and then one that you used to generate the previous run?
Are you sure you want wrapNearest on, by the way? Are you trying to simulate an unusually shaped unit cell?
Best,
Peter
> On Mar 30, 2016, at 4:49 PM, Daniela Rivas <dani.rivas.r_at_gmail.com> wrote:
>
> 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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