[gmx-users] Free energy calculation

[Justin Lemkul]

On 6/22/15 5:53 AM, nazli kashani javid wrote:
> Dear all
>
> I'm trying to calculate free energy of solvation according to Justin's
> tutorial for my protein in water.
>
> Is it true to follow that tutorial for my protein? any special changes in
> MDP file is necessary ?
>

You shouldn't use this method at all for a protein; the calculations will never 
converge.

> If there is no differences for systems to calculate free energy of
> solvation according to Justin's tutorial. I have set all my residue's
> charges to zero. and there is no ions into my solvent.
>

Don't do this.  The tutorial uses zero charges on methane because its stated 
purpose is to calculate *only* the vdW contribution to the free energy of 
solvation, and (as the tutorial says) it assumes the charges have already been 
scaled to zero, which is necessary for the full free energy of solvation.

Regardless, you shouldn't do this kind of calculation on a full protein.

-Justin

> I received this error several times during minimization (em_steep). Even
> when I change  some parameters in .mdp file such as pme_order or rvdw or
> vdw-type  and ...., the error didn't change.
>
>
> Fatal error:
> There is no domain decomposition for 10 nodes that is compatible with the
> given box and a minimum cell size of 4.2267 nm
> Change the number of nodes or mdrun option -rdd
> Look in the log file for details on the domain decomposition
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> I checked the website but I didn't get any helpful hint for my system.
>
> any help is appreciated.
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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