AMBER Archive (2002)

Subject: Re: md equilibration in chloroform

From: David A. Case (case_at_scripps.edu)
Date: Mon Jul 08 2002 - 10:42:24 CDT

On Mon, Jul 08, 2002, Sophia Kondratova wrote:

> I am having difficulties equilibrating a ligand/receptor complex in a
> chloroform box. I need to equilibrate the system to 300K in an NPT ensemble
> with SHAKE. What value of COMP(compressibility of the system) should I be
> using? ( 700 chcl3 in the box, 50.7410000 49.2030000 50.8920000 dimensions)
> If anyone has done chloroform simulations, maybe they could tell me what
> parameters are used to correctly equilibrate a chloroform box. Should I
> equilibrate first using an NVT ensemble? The error message that I get when I
> try to equilibrate:
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 3 2956 3651 3649
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>

For any type of solvent, you must equilibrate at constant volume to room
temperature before trying to do constant pressure simulations.

It doesn't matter much what you put in for the compressibility: this just
interacts with the time constant (taup) to determine how quickly the volume
adjusts to the instantaneous pressure. Using the water value should work
OK.

..good luck....dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
==================================================================