VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Aug 23 2006 - 09:32:39 CDT

Hi Pavan,
you should probably address this sort of inquiry to namd-l, not vmd-l.
To answer your specific question, though, if you are using pressure
control, after your first run you should comment out the periodic cell
definition and replace it with
extendedSystem xscfile
Where xscfile is the extended system file written by your previous
simulation, which has updated periodic cell information.
Peter

Pavan Ghatty wrote:
> Hello all,
>
> I started off with a protein in water. Minimized it (1000 steps),
> performed temperature rescaling (1000 steps) and then a 6ns NPT
> simulation. All went well. I then used the output of the 6ns NPT run
> to perform another 6ns NPT run (restarting essentially). But then the
> run crashed complaining about the "ERROR: Constraint failure in RATTLE
> algorithm for atom ". I checked in the archive for related problems
> and found the following fixes:
>
> On Tue, 5 Apr 2005, Marc Q. Ma wrote:
>
> /> Dear Nicholas, /
> /> /
> /> timestep 2.0 /
> /> stepsPerCycle 8 /
> /> nonBondedFreq 2 /
> /> fullElectFrequency 4 /
> /> /
> /> The above configuration will not work at all. What it gives is as
> follows: /
> /> /
> /> 1. You are using the Impulse multiple time stepping integrator,
> also called /
> /> Verlet-I/r-RESPA. This integrator has been shown to be stable when
> outer most /
> /> time step is 6fs with rigid bonds and rigid waters. However, for
> your long /
> /> simulation, ~1ns, the numerical resonance and nonlinear resonance
> will make /
> /> the simulation very unstable even at 6fs. For these long
> simulations, I would /
> /> suggest to use outermost timestep not more than 4fs. (FYI - I have
> some /
> /> publications on the stability issues on the Impulse integrator, eg. /
> /> Q. Ma, J. Izaguirre and R. Skeel, Verlet-I/r-RESPA/Impulse is
> limited by /
> /> nonlinear instability, SIAM J. Sci. Comput., 24(6):1951-1973, 2003. /
> /> /
> /> The discussion in the paper was made for constant energy
> simulation. However, /
> /> it gives good indication for other ensembles as well. /
> /> /
> /> 2. The above configuration gives you: leapfrog (innermost
> integrator) 2fs, /
> /> Impulse level 2 (middle integrator) for short range nonbonded
> forces (LJ and /
> /> Coulombic) 2.0*2 = 4fs, and Impulse level 3 (outermost integrator)
> for long /
> /> range nonbonded forces, 2.0*4 = 8fs! /
> /> /
> /> For Impulse, 8fs timestep is not attainable even with rigid water. /
> /> /
> /> 3. Simple fix --> change to timestep 1.0 and keep everything else.
> This should /
> /> make your outermost timestep to 4, and should be OK for long
> simulations. /
> /> /
> /> 4. Or, keep timestep 2.0, make nonBondedFreq 1, and fullElectFreq
> 2. This /
> /> should make your simulation go faster although asymptotically the
> running time /
> /> is on the same order. /
> /> /
> /> Hope this helps. Good luck! /
> /> /
> /> Marc /
> /> On Apr 5, 2005, at 6:33 AM, Nicholas M Glykos wrote:
>
> Now, I tried all the fixes but it just wouldn't run.... at that point
> I found that I was using the same input file, which is attached,
> without changing the cellbasisvector values. The values initially were
> 91, 89 and 89 along x, y and z axes. I then found the box dimensions
> from the output of the 6ns run and changed them to the new values
> which were, 87.9, 100.7 and 87.5 . The simulation is now running fine.
> Now, the question is, should I have done something else or is what I
> did the right thing. Also, is there a better way. Mighty Thanks for
> any suggestions/comments .
>
> --------------------------------------------------------------
> INPUT FILE
> ---------------------------------------------------------------
> firsttimestep 0
>
> # -------------
> # Force field
> # -------------
> paratypecharmm on
> parameters ../par_all27_prot_lipid.prm
>
> # ------------------
> # Molecular system
> # ------------------
> structure ../ionxlor.psf
>
> # -----------------
> # Initialization
> # -----------------
> {
> temperature 310.0
> coordinates coordiates.file
> cellBasisVector1 87.9 0.0 0.0
> cellBasisVector2 0.0 100.7 0.0
> cellBasisVector3 0.0 0.0 87.5
> cellOrigin 0.0 0.0 0.0
> }
> wrapall on
>
> # -------------------
> # MD Approximations
> # -------------------
> switching on # vdw: switch function, charge: shift
> function
> switchdist 10 # cutoff starting to smooth
> cutoff 12 # cutoff ending to smooth
> pairlistdist 14 # cutoff for nonbonded neighbor list
> stepspercycle 2 # neighbour list updating frequency
> exclude scaled1-4 # 1-2,1-3,1-4 interactions are excluded
> 1-4scaling 1.0 # 1.0 for Charmm, 0.8333 for Amber
> margin 1.0 # adjust cell size for NPT
> #PME on
> #PMEGridSizeX 72
> #PMEGridSizeY 72
> #PMEGridSizeZ 72
>
> # ---------------
> # MD integrator
> # ---------------
> seed 31415 # for starting a MD
> timestep 2.0 # integration step, fs
> nonbondedFreq 1 # timesteps between nonbonded evaluation
> fullElectFrequency 4 # timesteps for full elec. calculation
> rigidBonds all # all X-H bonds are constrained
> useSettle on # Settle algorithm for water
>
> langevin on # langevin dynamics
> langevinTemp 310.0 # target temperature
> langevinDamping 1.0 # damping coefficient of 1/ps
> {
> useGroupPressure yes # needed for rigid bonds
> useFlexibleCell no # no for water box, yes for membrane
> useConstantArea no # no for water box, maybe for meebrane
> useConstantRatio no # x-y ratio constant while x,y,z change
>
> LangevinPiston on
> LangevinPistonTarget 1.0325 # pressure in bar -> 1 atm
> LangevinPistonPeriod 200 # ocillation period around 200 fs
> LangevinPistonDecay 100 # ocillation decay time of 100 fs
> LangevinPistonTemp 310.0 # the same as langevinTemp
> }
>
> # --------
> # output
> # --------
> dcdfile dcdfile
> dcdunitcell yes
>
> restartname restart
> restartsave yes
>
> dcdfreq 20
> xstfreq 20
> restartfreq 50
>
> binaryrestart no # all restart file no binary
> binaryoutput no # all outputs no binary
>
> outputname output
> outputEnergies 20
> outputPressure 20
> outputtiming 20
>
> # --------
> # script
> # --------
> run 100
>
>
> /