[gmx-users] pbc whole
carlajamous at gmail.com
Thu Feb 18 15:53:29 CET 2010
Hi Justin and Tsjerk,
Thank you for your answers, but I found a command that worked for me:)
First, I concatenated the ensemble of my trajectory.
& then, I did the following:
trjconv -s a.tpr -f traj.xtc -o traj1.xtc -pbc nojump -n b.ndx
On Thu, Feb 18, 2010 at 12:47 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Carla Jamous wrote:
>> Hi Tsjerk,
>> sorry I didn't understand this part of your explanation:"Can you make an
>> image of the last frame and send a link
>> to it?"
> Render an image of your system from the end of your trajectory and post it
> somewhere online (like photobucket); do not send it as an attachment to your
> But anyhow, please can you send me the version of trjconv that does the
>> On Thu, Feb 18, 2010 at 11:42 AM, Tsjerk Wassenaar <tsjerkw at gmail.com<mailto:
>> tsjerkw at gmail.com>> wrote:
>> Hi Carla,
>> > I checked with genconf & now I'm certain that my ATP molecule is
>> still with
>> > the protein
>> That's good to know :)
>> >>> trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol
>> >>> (centering on "Protein")
>> So what did come out of this then? It should have given you a compact
>> representation of your system with the protein in the center. But if
>> the protein's in the center and everything is put as close to that
>> center as possible, which is what "compact" does, then the ATP should
>> be there too. Can you make an image of the last frame and send a link
>> to it? Alternatively, I have a patched version of trjconv that you can
>> use to do the trick. I can send it if you want.
>> Tsjerk A. Wassenaar, Ph.D.
>> Computational Chemist
>> Medicinal Chemist
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> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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