[gmx-users] Potential of mean force

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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