Re: cell size

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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