[gmx-users] Free energy calculation

[nazli kashani javid]

I'm trying to show thermodynamic stabilities of my protein from free energy
simulation. And I chose free energy of solvation, so if I can't use this
method how can I show thermodynamic stabilities of my protein?



On Mon, Jun 22, 2015 at 3:40 PM, nazli kashani javid <nazlikjavid at gmail.com>
wrote:

> 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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>
>