thank you
On Thu, Jul 17, 2014 at 11:31 AM, Brian Radak <radak004.umn.edu> wrote:
> imin = 5 requires that a trajectory (*i.e.* a mdcrd file, likely with many
> frames) is provided via the "-y" argument and operates sequentially on the
> structures it reads from that file. I believe a inpcrd file (or a restrt
> file, which contains the same information in a similar format) is still
> required, but only to get box information (this matters if you are using
> Ewald sums).
>
> An essentially equivalent procedure is to break up the mdcrd file into many
> inpcrd files and then run a separate calculation for each frame using imin
> = 1 and passing the structure to "-c". You will not need to use "-y" in
> this case.
>
> In this way, imin = 5 is almost entirely a convenience option.
>
> Regards,
> Brian
>
>
> On Thu, Jul 17, 2014 at 11:12 AM, Lara rajam <lara.4884.gmail.com> wrote:
>
> > Dear Amber
> >
> > I would like to post process the trajectory file.
> >
> > I want to minimize each frame in the mdcrd file that I got .
> >
> > I checked the earlier mails , I have a question.
> >
> > one should convert each frame to a rst file and it has to be given
> > separately using
> > the imin=5 option or it can be done for the whole trajectory with the
> mdcrd
> > file as a single run .
> >
> >
> >
> > suggestions will help me in understanding
> >
> > thank you
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Center for
> Integrative Proteomics Room 308
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Received on Thu Jul 17 2014 - 09:30:03 PDT
