From: ipsita basu (ibasu788_at_gmail.com)
Date: Mon Feb 01 2010 - 23:52:03 CST
Dear all,
I use rigidbonds and settle on. So please tell me what should be
done to solve it.
On 2/1/10, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
> 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.
>
-- Ipsita Basu Research Fellow c/o : Dr. Chaitali Mukhopadhyay Rajabazar Science College 92 APC Road Kolkata - 700009
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