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
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
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Received on Thu Jul 17 2014 - 09:00:02 PDT
