From: Aron Broom (broomsday_at_gmail.com)
Date: Tue Dec 13 2011 - 10:03:58 CST
I'm not sure if this is the issue, but if a water molecule approaches the
boundary, and one hydrogen goes out of the unit cell, but the center of
mass is still within the unit cell, it will have coordinates such that the
hydrogen is outside the unit cell. There is an option (maybe wrapALL on)
that will change this behavior (I could be wrong on that, never tried it).
Obviously your coordinates will look a bit messed up at that point. But
note that the normal behavior in NAMD is appropriate for a periodic cell,
those atoms that are outside the box in yoru output coordinate file are
treated as though they had wrapped around during all the MD steps.
~Aron
On Tue, Dec 13, 2011 at 10:47 AM, Hasan haska <hasanhaska_at_yahoo.com> wrote:
>
> ------------------------------
> *From:* Hasan haska <hasanhaska_at_yahoo.com>
> *To:* Axel Kohlmeyer <akohlmey_at_gmail.com>
> *Sent:* Tuesday, December 13, 2011 5:46 PM
> *Subject:* Re: namd-l: cell size
>
> Dear Axel,
>
> I modified the conf file like in below and run a short md but I still got
> the some water molecules' coordinates outside the box. I think this is
> normal since I use PBC. Is there any other way to get the coordinates *in
> a periodic box* ( 40 40 65 ) ?
>
> Thanks for your help.
> **
>
> useGroupPressure no
> useFlexibleCell no
> useConstantArea no
>
> ------------------------------
> *From:* Axel Kohlmeyer <akohlmey_at_gmail.com>
> *To:* Hasan haska <hasanhaska_at_yahoo.com>
> *Cc:* "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
> *Sent:* Tuesday, December 13, 2011 4:21 PM
> *Subject:* Re: namd-l: cell size
>
> On Tue, Dec 13, 2011 at 9:10 AM, Hasan haska <hasanhaska_at_yahoo.com> wrote:
> > Dear Namd Users,
> >
> > I run 5 ns md simulation for water molecules with the conf file below.
> And I
> > want to get the final coordinates of all water molecules in defined cell
> > sizes ( 40 40 65 ) . How can I do this operation in NAMD ?
>
> don't use a flexible cell?
>
> axel.
>
> >
> > Thank you very much for your help.
> >
> > Regards.
> >
> > *********
> > #--- This is a test namd configuration file
> >
> > paratypeCharmm on
> > parameters water.prm
> >
> > structure water.psf
> > coordinates water.pdb
> > outputName water_1out
> >
> > set temperature 300
> > temperature $temperature
> >
> >
> > firsttimestep 0
> >
> > # Integrator Parameters
> > timestep 1
> > nonbondedFreq 1
> > fullElectFrequency 5
> > stepspercycle 10
> >
> >
> >
> >
> > # Force-Field Parameters
> > exclude scaled1-4
> > 1-4scaling 0.8333333
> > cutoff 19.7
> > switching on
> > switchdist 17
> > pairlistdist 24
> >
> >
> >
> > # Constant Temperature Control
> > langevin on ;# do langevin dynamics
> > langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> > langevinTemp $temperature
> > langevinHydrogen on ;# don't couple langevin bath to hydrogens
> >
> >
> > #--- PBC
> >
> >
> > cellBasisVector1 40. 0.0 0.0
> > cellBasisVector2 0.0 40. 0.0
> > cellBasisVector3 0.0 0.0 65.
> >
> > #--- PME
> >
> > dielectric 1
> > PME on
> > PMEGridSizeX 45
> > PMEGridSizeY 45
> > PMEGridSizeZ 72
> >
> > # Constant Preswaterre Control (variable volume)
> > useGroupPressure no
> > useFlexibleCell yes
> > useConstantArea yes
> >
> > langevinPiston on
> > langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> > langevinPistonPeriod 200.
> > langevinPistonDecay 100.
> > langevinPistonTemp $temperature
> >
> >
> > #--- Output & Restart
> >
> > binaryoutput no
> >
> > binaryrestart yes
> >
> > restartname water_restart
> > DCDfile water_out.dcd
> >
> >
> > restartfreq 1250
> > dcdfreq 1250
> > xstFreq 1250
> > outputEnergies 1250
> > forceDCDfreq 1250
> > outputPressure 1250
> > outputtiming 1250
> >
> > minimize 12500
> > reinitvels $temperature
> >
> > run 5000000
> >
> > *************
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>
>
>
>
>
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