From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Feb 01 2010 - 06:15:22 CST
On Mon, Feb 1, 2010 at 6:40 AM, ipsita basu <ibasu788_at_gmail.com> wrote:
> Dear all,
> I am running simulations using namd. My input is attached with
> it. When I see the final picture of my system in vmd, there are bonds
> between H and H in water molecules. I observe this for two systems. Please
> tell me what is the problem in my script. Please help me.
please learn to help yourself, instead of bombarding a mailing list
with all kinds of unreflected questions!
this is a rather frequent question and has been answered on this
list and on the vmd list many times. there is no problem with your
simulation.
hint:: there are multiple ways to constrain a water molecule,
so its internal coordinates do not change.
cheers,
axel.
>
>
> Thanking You
>
>
> Ipsita Basu
>
>
>
>
> --
> Ipsita Basu
> Research Fellow
> c/o : Dr. Chaitali Mukhopadhyay
> Rajabazar Science College
> 92 APC Road
> Kolkata - 700009
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com Institute for Computational Molecular Science College of Science and Technology Temple University, Philadelphia PA, USA.
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