Re: water structure

From: Axel Kohlmeyer (
Date: Mon Feb 01 2010 - 06:15:22 CST

On Mon, Feb 1, 2010 at 6:40 AM, ipsita basu <> 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

hint:: there are multiple ways to constrain a water molecule,
so its internal coordinates do not change.

> Thanking You
>                 Ipsita Basu
> --
> Ipsita Basu
> Research Fellow
> c/o : Dr. Chaitali Mukhopadhyay
> Rajabazar Science College
> 92 APC Road
> Kolkata - 700009

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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