On 5/21/12 8:10 PM, patrick wintrode wrote:
Hi.
I've been trying to build my system in gromacs and have run into a problem. On
my initial energy minimization after building the .go and .top files, I
inevitably get 1 atom that doesn't get below the specified fmax (fmax of 10 in
my case: the force on the atom is around 60-90). This remains true after
multiple rounds of minimization using both steepest descent and CG algorithms.
The atom in question is always a hydrogen at the D1 or E2 position in one of the
histidines. I've tried both letting pdb2gmx assign the histidine protonation
states and using proPKA to assign them and then making pdb2gmx use those
assignments with the -his tag.
So far nothing has worked. Any suggestions?
An emtol of 10 is very low for normal applications, and you're unlikely to
achieve it unless you're using double precision, a very small emstep, and/or
several rounds of steep/cg/l-bfgs minimization algorithms.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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