On Thu, Aug 18, 2011 at 6:47 PM, mirage . <m.o.m.live.fr> wrote:
>
> Hi Amber users,
> I want to count the number of hbond durig simulation, then i do rimage with
> ptraj like :
>
> trajin md.mdcrd
> center :1-3
> trajout reimaged.mdcrd
> image center familiar
>
> 1/ a part of my molecule is sometimes out of box !!! How to do correction?
>
Try this:
trajin md.mdcrd
center :1-3 mass origin
image origin familiar
trajout reimaged.mdcrd
Is your molecule just residues 1-3?
2/ is there any software like vmd to do this ?
>
ptraj can do it. So can cpptraj. WHen you say "software like VMD" do you
mean a GUI?
> 3/ what is the complete and correct command to do this with vmd
>
You'd be better off asking the VMD people. They have their own mailing list
for questions like that.
HTH,
Jason
>
> Thanks in advance for any help
>
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Aug 18 2011 - 18:00:02 PDT
