[gmx-users] Potential of mean force

Justin A. Lemkul jalemkul at vt.edu
Wed May 25 12:59:37 CEST 2011

Mark Abraham wrote:
> On 25/05/11, *郭漫 * <pysgm2010 at hotmail.com> wrote:
>> Hello users,
>> I followed the tutorial steps to do umbrella sampling of GROMACS 
>> Tutorial, (This is the tutorial site 
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html) 
>> and get the PMF is close to -50 kcal/mol. However, when I put 
>> amber99sb parameter instead of gromos96 53a6 parameter, without 
>> changing the other parameters and steps,the result is about -35 
>> kcal/mol. I don't know why the difference is so large between them, 
>> and i need your help for explaining what is the reason for the 
>> difference, simply because I changed the force filed, or some other 
>> possible causes.
> If all you've changed is the force field, and these simulations are long 
> enough to produce converged measurements, then "welcome to the jungle". 
> Different force fields have been demonstrated to be good or bad on 
> different types of systems for different types of properties. Choosing 
> the right force field is normally a most important and sometimes the 
> most time-consuming part of doing simulations properly. Read widely, and 
> take good notes.

Agreed.  Also important to note is that simply changing the force field and not 
adjusting any of the .mdp settings (as would be required for proper use of a 
different force field) could result in incorrect use of the new force field.  I 
don't often use the Amber force fields, but I believe different cutoffs and 
neighborsearching intervals should be used.  The parameters given are for Gromos96.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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