Re: hydrogens collapsing

From: Brian Bennion (
Date: Tue Jan 18 2005 - 10:23:40 CST


I am a little surprised that you found parameters so similiar to

There are some parameters missing or more likely they are incorrect. My
guess is that the H-C-C angle force constant is not large enough to
balance the H-C-C-X dihedral terms.

Just my $0.02


 On Tue, 18 Jan 2005

> Hi,
> I am trying to simulate a system with the estrogen receptor and its natural
> ligand estradiol (a steroid). I have found cholesterol parameters, which
> together with the CHARMM prot_lipid forcefield should be able to create most
> steroids.
> My problem is, that when I try to minimize, heat or whatever I want to do the
> hydrogens are collapsing. Eg. three hydrogens in a methyl group obtains same
> coordinates after about 300 steps of minimization of heating of the system.
> The problem is not with the parameters since I have been able to minimize the
> system using CHARMM without the hydrogens collapsing.
> Do you have any ideas to what I can do? I can not imagine anything else to
> try...
> Thanks in advance
> Leyla

**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:40:29 CST