[gmx-users] Large forces on HIS hydrogen atoms

Justin A. Lemkul jalemkul at vt.edu
Mon May 21 20:18:16 CEST 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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