VMD-L Mailing List

From: Ramya Gamini (ramyabhargavi_at_gmail.com)
Date: Wed Dec 01 2010 - 11:37:26 CST

Hi Buddhadev,

Use the PBCTools plugin
You can do post processing using the pbc unwrap command:

Load the entire trajectory, and make sure you are at the first frame

on TkConsole type,

pbc unwrap -sel "protein"

Hope it helps,
Ramya

On Mon, Nov 29, 2010 at 1:41 PM, Buddhadev Maiti <chebm_at_langate.gsu.edu>wrote:

> Dear NAMD users,
>
> I recently ran some NPT simulations on a very large system composed by
> different subunits.
> What happens is that sometimes a part of the system comes out of the water
> box so that
> due to the wrapping procedure, one of the subunits is reflected on the
> opposite side of the box.
> Obviously in my following simulations I disabled the wrapping command and I
> also used a larger
> water box. However, I don't want to waste my old work, so I was wondering
> if there is any
> post-processing of the trajectory that I can use to fix the problem.
>
> So far I tried to address the problem using ptraj. here is my script:
>
> trajin file-in.dcd
> trajout file-out.dcd CHARMM
> center :1-9854 mass origin
> image origin center
>
> However this script does not always work. Sometimes I have to use an
> alternative script:
>
> trajin file-in.dcd
> trajout file-out.dcd CHARMM
> center :1-9854 mass origin
>
> Unfortunately, there are situations when neither of these scripts work.
> The simulations I am tryiong to analyze have all been performed in the
> same way, so there is no general rule that I could figure out as to when
> one script is more suitable than the other. Can anyone help me ?
> Is there any reliable post-processing strategy to correct the wrapping
> problems ?
>
> Thanks for your help,
>
> Maiti
>
>
>