From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Mar 04 2013 - 06:10:43 CST
On Mon, Mar 4, 2013 at 12:55 PM, Mihaela Drenscko <quo.physics_at_gmail.com> wrote:
> 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?
no. it takes so long because it takes 0.7 seconds to compute one time step.
axel.
>
> 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
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy.
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