Re: restart problem

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Jan 05 2011 - 14:23:32 CST

SMD forces are calculated based on the timestep. Because when you restarted, you reset the timestep to 0, the forces are significantly larger. You need to set "firsttimestep 500000" in your NAMD configuration file for the restarted run.

On Jan 5, 2011, at 2:07 AM, charlie wrote:

> Hello , users
> I run 500000 steps , then 300000 steps .But as can be seen below, the force is not continuous between the first run and the restart.
>
> SMDTITLE: TS CURRENT_POSITION FORCE
> SMD 500000 25.8631 33.7159 25.5426 -96.3874 265.343 285.517
>
> SMDTITLE: TS CURRENT_POSITION FORCE
> SMD 0 26.4281 34.7389 24.6329 1058.71 -2914.5 -3136.08
>
> What's the problem ? Thanks and best wishes.
>
> My restart configure file is
> #######configure file #######################################
> set inputname smd
> structure ionized.psf
> coordinates ionized.ref
> bincoordinates $inputname.restart.coor
> binVelocities $inputname.restart.vel
> extendedSystem $inputname.restart.xsc
> outputName smd_relay
> set temperature 310
> firsttimestep 0
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
> # Input
> paraTypeCharmm on
> parameters par_all27_prot_lipid.inp
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 13.5
> # Integrator Parameters
> timestep 2.0 ;# 2fs/step
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
> langevinHydrogen no ;# don't couple langevin bath to hydrogens
> # Output
> binaryoutput no
> dcdfreq 500 ;# 500steps = every 1ps
> outputEnergies 100
> # Fixed Atoms Constraint (set PDB beta-column to 1)
> if {1} {
> fixedAtoms on
> fixedAtomsFile ionized.ref
> fixedAtomsCol B
> }
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
> # Put here any custom parameters that are specific to
> # this job (e.g., SMD, TclForces, etc...)
> SMD on
> SMDFile ionized.ref
> SMDk 7
> SMDVel 0.00002
> SMDDir -0.24005720076537967 0.6608481549127442 0.7110922981646699
> SMDOutputFreq 500
>
> run 300000
>
>

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