[gmx-users] Free energy calculation

[nazli kashani javid]

thanks for your clear answer.

Is there any reasonable method for calculating free energy of solvation for
my protein? :-(





On Mon, Jun 22, 2015 at 2:26 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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