<HTML><HEAD><META content="text/html; charset=x-user-defined" http-equiv="Content-Type"><style type="text/css"><!--.MailHeader { font-family: "Arial"; font-size: 8pt; color: #000000; font-style: normal; font-weight: normal; text-decoration: none; }//--></style></HEAD><BODY>Dear all,<br>
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?<br>
Looking forward to your kind reply.<br>
<br>
Rahul Karyappa<br>
NCL, Pune<br>
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