Re: Very long simulation

From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Mon Mar 04 2013 - 17:39:26 CST

Hi.

try to put less decimal places at your PBC parameters, e.g. 46.3 instead 46.2735

Regards

Flavio

------------------------------
Em seg, 4 de mar de 2013 11:55 GMT Mihaela Drenscko escreveu:

>Hi,
>
>I am running a DMPC simulation since yesterday, and it says, "TIMING:
>47500 CPU: 39142.3, 0.699396/step Wall: 39142.3, 0.699396/step,
>39.5353 hours remaining, 57.136719 MB of memory in use."
>I used the following comands to create a pdb file for fixed atoms:
>
>set all [atomselect top all]
>set fix [atomselect top "protein and name N"]
>set fix [atomselect top protein and backbone]
>after that, you have to type the following:
>$all set beta 0
>$fix set beta 1
>$all writepdb dmpcf.pdb
>
>And this is the conf file:
>
>In the program is was recommended that I run minimization 250, 000
>steps. Is this the reason the simulation is so long?
>
>Thank you,
>
>Mihaela
>
>#############################################################
>## ADJUSTABLE PARAMETERS ##
>#############################################################
>
>structure ../DMPC/dmpc_autopsf.psf
>coordinates ../DMPC/dmpc.pdb
>outputName dmpcout
>
>set temperature 300
>
>
>#############################################################
>## SIMULATION PARAMETERS ##
>#############################################################
>
># Input
>paraTypeCharmm on
>parameters par_all36_lipid.prm
>parameters par_all27_prot_lipid.inp
>
>
># NOTE: Do not set the initial velocity temperature if you
># have also specified a .vel restart file!
>temperature $temperature
>
>
># Periodic Boundary Conditions
># NOTE: Do not set the periodic cell basis if you have also
># specified an .xsc restart file!
>if {1} {
>cellBasisVector1 46.2735 0. 0.
>cellBasisVector2 0. 46.2735 0.
>cellBasisVector3 0. 0. 62.3748
>cellOrigin 0. 0. 0.
>}
>wrapWater on
>wrapAll on
>
>
># Force-Field Parameters
>exclude scaled1-4
>1-4scaling 1.0
>cutoff 12.
>switching on
>switchdist 10.
>pairlistdist 13.5
>vdwForceSwitching on
>
>
>
># Integrator Parameters
>timestep 2.0 ;# 2fs/step
>rigidBonds all ;# needed for 2fs steps
>nonbondedFreq 1
>fullElectFrequency 2
>stepspercycle 20
>
>
>#PME (for full-system periodic electrostatics)
>if {1} {
>PME yes
>PMEGridSizeX 50
>PMEGridSizeY 50
>PMEGridSizeZ 65
>}
>
>
># Constant Temperature Control
>langevin on ;# do langevin dynamics
>langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
>langevinTemp $temperature
>
># Constant Pressure Control (variable volume)
>if {0} {
>useGroupPressure yes ;# needed for 2fs steps
>useFlexibleCell yes ;# no for water box, yes for membrane
>useConstantArea no ;# no for water box, yes for membrane
>
>langevinPiston on
>langevinPistonTarget 1.01325 ;# in bar -> 1 atm
>langevinPistonPeriod 200.
>langevinPistonDecay 50.
>langevinPistonTemp $temperature
>}
>
>
>restartfreq 1000 ;# 1000steps = every 2ps
>dcdfreq 1000
>xstFreq 1000
>outputEnergies 50
>outputPressure 50
>
>
># Fixed Atoms Constraint (set PDB beta-column to 1)
>if {1} {
>fixedAtoms on
>fixedAtomsFile dmpcf.pdb
>fixedAtomsCol B
>fixedAtomsForces on
>}
>
>#############################################################
>## EXTRA PARAMETERS ##
>#############################################################
>
># Put here any custom parameters that are specific to
># this job (e.g., SMD, TclForces, etc...)
>
>#############################################################
>## EXECUTION SCRIPT ##
>#############################################################
>
># Minimization
>if {1} {
>minimize 1000
>reinitvels $temperature
>}
>
>run 250000 ;# 0.5 ns
>

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