RE: AMBER: problem with pressure equilibration

From: Ross Walker <>
Date: Thu, 27 Jan 2005 14:45:20 -0800

Dear Cenk,

>BOND = 222354.5092

This is HUGE... Your system has obviously blown up. Try writing the
coordinate file every step and then you can watch and see what happens.

I suspect that something is very wrong with the structure from the constant
volume simulation. Check this carefully. If you can post that output file
that would be helpful as well. It is possible that your initial system was
highly compressed and so as soon as you remove the constraints of being
fixed to a certain volume it expanded extremely rapidly (i.e. an explosion).
This would imply that your initial structure, from which you did the
constant volume simulation, was overly compressed. You will need to go back
and check this.

> imin=0, nstlim=200,
> dt=0.002, cut=5, irest=1, ntx=7,

Alternatively it could be due to cut=5...!!! Do you really mean to use a 5
angstrom cutoff???

> Group input for restrained neamine
> 100.0
> RES 1

Your restraints may also be causing you a problem. But I would check the
other things first.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Thu Jan 27 2005 - 22:53:01 PST
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