From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Sun Sep 04 2005 - 18:12:59 CDT
Anna,
You shouldn't have to repeat your simulation. You should have your .xst
file which contains all of the unit cell information, hopefully written at
the same frequency as the dcd file.
Using pbctools,
http://www.ks.uiuc.edu/Research/vmd/script_library/
you should be able to load in your unit cell info into VMD. I am not
exactly sure what you are doing now, although it seems interesting. I
have only used pbctools along with pbcwrap to visualize my periodic
boundary conditions (when I didn't know about 'DCDUnitCell on').
Maybe your simulation was short, and you may not want to fool with this.
I write all my unit cell info to the dcd file. It makes analysis much
easier.
Josh
On Fri, September 2, 2005 4:58 am, Anna Modzelewska wrote:
> Thank you very much!
> I didn't know the option DCDUnitCell. As far as I understand if this
> option wasn't active I can not calculate pair interaction energy
> correctly? I should repeat the simulation?
>
> What about velocities? Should I precise the restart.vel file for pair
> interactions calculations or just set the temperature?
>
> Regards
> Anna
> ----- Original Message -----
> From: Philip Fowler
> To: Anna Modzelewska ; namd-l_at_ks.uiuc.edu
> Sent: Friday, September 02, 2005 9:22 AM
> Subject: Re: namd-l: pair interactions in NPT
>
>
> Anna,
>
> The way to do this is to include the unitcell info in the DCD using
> DCDUnitCell on in the NAMD input file (I believe that this on by the
> default for NAMD2.5 and later). Then when you read the DCD back into
> NAMD to calculate the pair interaction energy NAMD retrieves the
> CellBasisVectors from the DCD file itself and correctly wraps the
> water etc. This would be pretty obvious if it got it wrong as it is
> likely NAMD would at some point try wrapping a water on top of
> another water and infinite energies would start to appear.
>
> If you ran multiple simulations and then concatenated the DCDs using
> catdcd, then your problem may be that the catdcd supplied with NAMD
> strips out the unitcell info from the
> DCD files. If this is the case you will need to recompile catdcd as
> described in the thread below.
>
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/2574.html
>
> --Phil
>
>
>
> > Hi,
> > I need to calculate pair interaction energy after a simulation in
> > NPT. For each sets of coordinates from a dcd file I have different
> > sets of CellBasisVectors. I took the script below and I adopted it
> > in the way that it changes not only the fistTimestep but also the
> > CellVectors. It didn't work!
> > After several modifications I discovered that NAMD can not change
> > vectors values during a simulation (it stops with information
> > "FATAL ERROR: Setting parameter cellBasisVector1 from script failed").
> > I absolutely need to calculate the interaction energy for my
> > simulations, what can I do?
> >
> > Any help will be very appreciated!
> > Anna
> >
> >
> > "coorfile open dcd name.dcd
> >
> > set ts 0
> > while { [coorfile read] != -1 } {
> > incr ts
> > firstTimestep $ts
> > run 0
> > }
> > coorfile close"
> >
> >
> >
> >
>
--------------------------------------------------
Joshua D. Moore
Graduate Student
North Carolina State University
Department of Chemical and Biomolecular Engineering
Box 7905 Centennial Campus
Engineering Building I
911 Partners Way
Raleigh, NC 27695-7905
Phone: (919) 513-2051
Fax: (919) 513-2470
Email: jdmoore_at_unity.ncsu.edu
--------------------------------------------------
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