Re: bunch of water molecules

From: Jerome Henin (
Date: Thu Aug 09 2007 - 15:03:12 CDT

Hi Sathish:
Look for the keyword "rigidBonds" in your input file. Starting from there and
using the docs, you should be able to figure out what's happening.

On Thursday 09 August 2007 14:39, sathish kumar gurupatham wrote:
> hi all,
> i am simulating a bunch of water molecules at 310k.( to learn namd)
> I am getting a lot of fluctuations during minimisation for angle and bond
> potentials
> but at the end they reduce to zero (suddenly).
> and during equilibration they remain zero through out.
> is right?
> does it mean the molecules do not have angle and bond potentials?
> if yes, how? i wrong in simulation?
> please help me learn the basics.
> thanks in advance.
> sathish.

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