Hi,
Use energy post-processing (imin=5) with energy minimization options
set as you want them in sander. See manual for more details.
-Dan
On Sat, Nov 25, 2017 at 10:24 PM, Abdul-Rashid III Sampaco
<absampaco.up.edu.ph> wrote:
> Hello,
>
> I have a 1000ns netcdf trajectory file (i wrote a new structure every 1ps
> so the file contains 1 million structures). It is basically a
> conformational search of a small peptide. Is it possible to perform energy
> minimization on all the structures in the file without having to rewrite
> each one to a new file and iterating over them with a separate sander
> command? Thanks.
>
> I have already tried using the nc file as an input to sander like as
> follows:
>
> sander -O -i min.in -o min.out -c md.nc -r min_md.rst -p md.parm7
>
> It turns out sander only accepts crd and rst7 files.
>
>
> Rashid
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Sat Nov 25 2017 - 20:00:03 PST
