From: Ilya Chorny (ichorny_at_gmail.com)
Date: Sat Oct 06 2007 - 10:30:25 CDT
Yeah it makes sense, though it should not matter. A way to maintain
temperature is to reinitialize ever so often. I don't believe I am
reinitializing my velocities though because I provide a .restart.vel file.
On 10/5/07, Richard Wood <rwoodphd_at_yahoo.com> wrote:
>
> Ilya,
>
> When you restart, your "distribution" of velocities should behave as they
> did before your calculation stopped; in other words, when you restart, the
> velocity distribution should appear as if you never restarted the
> calculation, and should look as if it had been going continuously.
>
> Put another way, your "instantaneous" velocity for each atom when you
> restart should be the same velocity that rach had when your calculation
> ended.
>
> Does this make sense?
>
> Richard
>
>
> Richard L. Wood, Ph. D.
> University of Minnesota
> Dept. of Medicinal Chemistry,
> College of Pharmacy
> 717 Delaware St. SE
> Minneapolis, MN 55414-2959
> rwoodphd_at_yahoo.com
>
> ----- Original Message ----
> From: Ilya Chorny <ichorny_at_gmail.com>
> To: NAMD list <namd-l_at_ks.uiuc.edu>
> Sent: Friday, October 5, 2007 3:02:51 PM
> Subject: Re: namd-l: Charmm 22 vs Charmm 27
>
> Below is configuration file. Does any one see any obvious mistakes? Can
> reinitializing the velocities when I restart a run cause the protein to fall
> apart?
>
> Thanks,
>
> Ilya
>
>
> structure addions.psf
> coordinates addions.pdb
> Bincoordinates Prot_free4.restart.coor
> Binvelocities Prot_free4.restart.vel
> ExtendedSystem Prot_free4.restart.xsc
>
> set temperature 310
> set outputname Prot_free5
> binaryoutput no
>
> #firsttimestep 0
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters //winsc/share/namd/c31b1/par_all27_prot_lipid.prm
> #temperature $temperature
>
>
> # Force-Field Parameters
> exclude 1-4
> 1-4scaling 1.0
> cutoff 12.0
> switching off
> switchdist 10.5
> pairlistdist 12.5
>
>
> # 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 off ;# don't couple langevin bath to hydrogens
>
>
> # Periodic Boundary Conditions
> #cellBasisVector1 117 0. 0.
> #cellBasisVector2 0. 117. 0.
> #cellBasisVector3 0. 0 92.
> #cellOrigin 10.09 9.73 -0.71
>
> wrapAll on
>
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 128
> PMEGridSizeY 128
> PMEGridSizeZ 128
>
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes ;# needed for rigidBonds
> useFlexibleCell yes
> useConstantRatio yes
> zeroMomentum yes
>
> langevinPiston yes
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 200.
> langevinPistonDecay 100.
> langevinPistonTemp $temperature
>
>
> # Output
> outputName $outputname
>
> restartfreq 500 ;# 500steps = every 1ps
> dcdfreq 500
> xstFreq 500
> outputEnergies 500
> outputPressure 500
>
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> #Minimization
> #minimize 1000
> # margin 2.5
> reinitvels $temperature
> output NeRh50_free
> #run 2000000 ;# 2ns
> #run 1223500 ;# 2ns
> #run 906500 ;# 2ns
> #run 675500 ;# 2ns
> run 334000 ;# 2ns
>
>
>
>
> On 10/5/07, Ilya Chorny <ichorny_at_gmail.com> wrote:
> >
> > I am running a membrane protein simulation using the CHARMM 27
> > forcefield and I my protein seems to be falling apart. Could it be because I
> > am using CHARMM27 instead of CHARMM22? I am also using TIP3 and POPE.
> >
> > Thanks,
> >
> > Ilya
> >
> >
> > --
> > Ilya Chorny Ph.D.
> >
>
>
>
> --
> Ilya Chorny Ph.D.
>
>
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-- Ilya Chorny Ph.D.
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