Hi,
Try using the 'autoimage' command from cpptraj; it was specifically
designed to address this issue. Let me know if you have further
problems.
-Dan
On Thu, Aug 21, 2014 at 7:45 AM, Caitlin Scott <cescott.caltech.edu> wrote:
> Hi Everyone,
>
> I'm trying to run a NPT simulation of a dimer. There are two chains, each
> with residues numbered 1-93. When I set iwrap=1 and try to visualize the
> simulation in vmd, the two protein chains are separated and put into
> different corners of the waterbox. I'm trying to use cpptraj to put the
> dimer into the center of the waterbox with the following input file:
>
> trajin 01_Prod.cdf
> unwrap :1-2880 byatom
> center :1-2880 origin
> image origin center familiar
> trajout out.cdf cdf nobox
>
> This doesn't fix the problem--the two protein chains are still separated.
> Can someone please tell me what's wrong with the above *.in file or offer
> a suggestion on how to fix this issue?
>
> Caitlin
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Aug 21 2014 - 07:00:03 PDT
