From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Mar 31 2016 - 01:00:46 CDT
The data that causes the jump might just be data that was written after the last restart files have been written. So, as you restarted the simulation from a point in time, earlier than your simulation already was, you get a jump of course, as your system made a time travel. If this is the issue, you don't need to worry about: For analyzation purpose you could remove that abundant frames (e.g. catdcd) and data from the log files after the last restart writing (text editor).
Norman Geist
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Peter Freddolino
> Gesendet: Donnerstag, 31. März 2016 02:34
> An: Daniela Rivas <dani.rivas.r_at_gmail.com>
> Cc: namd-l_at_ks.uiuc.edu
> Betreff: Re: namd-l: "Jump" in Energy and Volume graphs of my MD
>
> Hi Daniela,
> Just so we’re clear, using wrapNearest is not the right answer just because
> you’re simulating a membrane protein, but rather, if you want to use a
> hexagonal unit cell.
>
> Could you post a diff of the original config file vs. the restart config file? The
> periodic cell dimensions have to be getting messed up somehow, I’m just
> not quite sure how. The last few lines of the .xst file from the first run, and
> the output .xsc file, would also be helpful.
> Thanks,
> Peter
>
> > On Mar 30, 2016, at 5:01 PM, Daniela Rivas <dani.rivas.r_at_gmail.com>
> wrote:
> >
> > Hi Peter,
> >
> > I'm attaching the graphs so you can take a better look and I'm using
> wrapNearest on because it is a membrane protein simulation.
> >
> > Thanks a lot.
> > Daniela.
> >
> > On Wed, Mar 30, 2016 at 5:56 PM, Peter Freddolino
> <petefred_at_umich.edu> wrote:
> > 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!
> > >
> > >
> >
> >
> > <Energia_Modelo.png><Volumen_Modelo.png>
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