[gmx-users] problem in viewing trajectory for the whole system

[Itamar Kass]

   Why not try vmd (http://www.ks.uiuc.edu/Research/vmd/)?  I use it all the
time.
 Itamar.


Quoting Rahul Karyappa <r.karyappa at ncl.res.in>:

>
> Dear all,
>
>    At last I successfully ran MD on my system (polymer +
> water + ions). But when I seen my trajectory, I am not able to see
> water molecules or the ions. I can see only the polymer chain. When I
> ran ngmx command, first it asks about group 1 and group 1. Then I
> selected both the groups. But the trajectory shows only polymer chain.
> What may be the problem?
>
> Looking forward to your kind reply.
>
>
> Rahul Karyappa
>
> NCL, Pune
>
>
>
>
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===========================================
| Itamar Kass
| The Alexander Silberman
| Institute of Life Sciences
| Department of Biological Chemistry
| The Hebrew University, Givat-Ram
| Jerusalem, 91904, Israel
| Tel: +972-(0)2-6585194
| Fax: +972-(0)2-6584329
| Email: ikass at cc.huji.ac.il
| Net: http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html
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