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

Rahul Karyappa r.karyappa at ncl.res.in
Fri Sep 9 13:36:12 CEST 2005

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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