AMBER Archive (2002)

Subject: md equilibration in chloroform

From: Sophia Kondratova (x357l_at_unb.ca)
Date: Mon Jul 08 2002 - 08:38:27 CDT

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.

Any help would be greatly appreciated.

Sophia Kondratova
Chemistry Department
University of New Brunswick
Canada