Re: restart a simulation

From: upayan baul (margheritan22_at_gmail.com)
Date: Fri Mar 16 2012 - 06:51:28 CDT

Thanks for the help!
-Upayan

On Fri, Mar 16, 2012 at 12:31 PM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:

> Hi Upayan,****
>
> ** **
>
> Remove the minimize command from the if clause. Namd will suddenly execute
> the minimize command as it reads it, but you didnít set all needed
> parameters till there. You also already set the minimize at the end of the
> script. I think namd will then also complain about setting the temperature
> AND reading velocities from restart, thatís nonsense. Also itís nonsense to
> load a velocity file, and then minimize as all velocities get lost then,
> thereís no need to minimize every run you restart, itís only for the
> initial structure to find the energy minimum and if the initial structure
> has bad contacts/bonds/angles etc. ****
>
> ** **
>
> Feel free to ask****
>
> ** **
>
> Norman Geist.****
>
> ** **
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *upayan baul
> *Gesendet:* Donnerstag, 15. Mšrz 2012 13:21
> *An:* namd-l_at_ks.uiuc.edu
> *Betreff:* namd-l: restart a simulation****
>
> ** **
>
> Hi,****
>
> I am very new to using NAMD. I am trying to equilibrate a box of water in
> steps. The first run works but I'm unable to restart it. Please point out
> my mistake. I attach the error message in log file too.****
>
> ** **
>
> The input files exist in the directory.****
>
> ** **
>
> Rehards,****
>
> Upayan****
>
> ** **
>
> ** **
>
> structure ../water/solvate.psf****
>
> coordinates ../water/solvate.pdb****
>
> ** **
>
> set temperature 298****
>
> set outputname wb_eq2****
>
> ** **
>
> # Continuing a job from the restart files****
>
> if {1} {****
>
> set inputname wb_eq1****
>
> binCoordinates $inputname.restart.coor****
>
> binVelocities $inputname.restart.vel****
>
> extendedSystem $inputname.restart.xsc ****
>
> ** **
>
> temperature $temperature****
>
> minimize 100****
>
> reinitvels $temperature****
>
> ** **
>
> }****
>
> ** **
>
> firsttimestep 200001****
>
> ** **
>
> ** **
>
> # Input****
>
> paraTypeCharmm on****
>
> parameters ../water/par_all27_prot_lipid.inp ****
>
> temperature $temperature****
>
> ** **
>
> ** **
>
> # Force-Field Parameters****
>
> exclude 1-3****
>
> #1-4scaling 1.0****
>
> cutoff 12.0****
>
> switching on****
>
> switchdist 10.0****
>
> pairlistdist 14.0****
>
> ** **
>
> ** **
>
> # Integrator Parameters****
>
> timestep 1.0 ;# 1fs/step****
>
> rigidBonds all ;# needed for 1fs steps****
>
> nonbondedFreq 1****
>
> fullElectFrequency 2 ****
>
> stepspercycle 10****
>
> ** **
>
> ** **
>
> # Constant Temperature Control****
>
> langevin on ;# do langevin dynamics****
>
> langevinDamping 1 ;# damping coefficient (gamma) of 1/ps****
>
> langevinTemp $temperature****
>
> langevinHydrogen off ;# don't couple langevin bath to hydrogens****
>
> ** **
>
> ** **
>
> # Periodic Boundary Conditions****
>
> cellBasisVector1 48.0 0. 0.0****
>
> cellBasisVector2 0.0 25.0 0.0****
>
> cellBasisVector3 0.0 0 48.0****
>
> cellOrigin 23.90 12.51 23.99****
>
> ** **
>
> wrapAll on****
>
> ** **
>
> ** **
>
> # PME (for full-system periodic electrostatics)****
>
> PME yes****
>
> #PMEGridSpacing 1.0****
>
> ** **
>
> #manual grid definition****
>
> PMEGridSizeX 60****
>
> PMEGridSizeY 60****
>
> PMEGridSizeZ 60****
>
> ** **
>
> ** **
>
> # Constant Pressure Control (variable volume)****
>
> useGroupPressure yes ;# needed for rigidBonds****
>
> useFlexibleCell no****
>
> useConstantArea no****
>
> ** **
>
> langevinPiston on****
>
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm****
>
> langevinPistonPeriod 100.0****
>
> langevinPistonDecay 50.0****
>
> langevinPistonTemp $temperature****
>
> ** **
>
> ** **
>
> # Output****
>
> outputName $outputname****
>
> ** **
>
> restartfreq 500 ****
>
> dcdfreq 500****
>
> xstFreq 500****
>
> outputEnergies 100****
>
> outputPressure 100****
>
> ** **
>
> ** **
>
> # Minimization****
>
> minimize 100****
>
> reinitvels $temperature****
>
> ** **
>
> run 200000 ;****
>
> ** **
>
> ** **
>
> log file:****
>
> Charm++: standalone mode (not using charmrun)****
>
> Charm++> cpu topology info is being gathered.****
>
> Charm++> Running on 1 unique compute nodes (2-way SMP).****
>
> Info: NAMD 2.7b2 for Linux-x86****
>
> Info: ****
>
> Info: Please visit http://www.ks.uiuc.edu/Research/namd/****
>
> Info: and send feedback or bug reports to namd_at_ks.uiuc.edu****
>
> Info: ****
>
> Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)****
>
> Info: in all publications reporting results obtained with NAMD.****
>
> Info: ****
>
> Info: Based on Charm++/Converse 60103 for net-linux-iccstatic****
>
> Info: Built Thu Nov 12 22:11:41 CST 2009 by jim on kyoto.ks.uiuc.edu****
>
> Info: 1 NAMD 2.7b2 Linux-x86 1 as38 upayanb****
>
> Info: Running on 1 processors.****
>
> Info: CPU topology information available.****
>
> Info: Charm++/Converse parallel runtime startup completed at 27360.5 s****
>
> Info: 1.22376 MB of memory in use based on CmiMemoryUsage****
>
> Info: Configuration file is wb_eq.conf****
>
> TCL: Suspending until startup complete.****
>
> ERROR: 'cutoff' is a required configuration option****
>
> ERROR: cutoff defines: local electrostatic and Vdw distance****
>
> ERROR: 'exclude' is a required configuration option****
>
> ERROR: exclude defines: Electrostatic exclusion policy****
>
> ERROR: 'outputname' is a required configuration option****
>
> ERROR: outputname defines: prefix for the final PDB position and
> velocity filenames****
>
> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE****
>
> [0] Stack Traceback:****
>
> [0] _ZN9NamdState14configListInitEP10ConfigList+0x369 [0x84aadcd]****
>
> [1] _ZN9ScriptTcl9initcheckEv+0x54 [0x84fd338]****
>
> ** **
>

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