From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Dec 13 2011 - 10:00:43 CST
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 ) ?
have you tried using wrapAll ?
http://www.ks.uiuc.edu/Research/namd/2.8/ug/node33.html
other than that, wrapping of coordinates
can easily done in post-processing, e.g.
using the pbctools plugin in VMD.
axel.
>
> 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.
>
>
>
>
-- 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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