[gmx-users] question regarding free energy calculations

[bipin singh]

Hello Dr. Justin,

So, the option "couple-intramol = yes" can be used to selectively turn off
vdw and coulombic interactions of only few atoms from the rest of the
molecule using a B state topology in Gromacs, as mentioned by Asaf.




On Thu, Dec 26, 2013 at 6:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/25/13, 4:55 AM, Asaf Farhi wrote:
>
>> Dear all
>>
>> Hi. We have a question regarding the implementation of free energy
>> calculations in Gromacs that we have been trying for long time to decipher.
>>
>> The question is the following:
>>
>> When transforming molecule A to B if the non bonded interactions are
>> changed through the topology file e.g:
>> [ atoms ]
>> ;  nr  type  resnr  resid  atom  cgnr  charge    mass   typeB  chargeB
>>  massB
>>      1    HC    1     PCH3    H1    1    0.123   1.0080   HC    0.0
>>  1.0080
>>
>> , will the the interactions of this atom with all the other atoms be
>> affected by this change of charge?
>>
>>
> That depends on how you are setting coupl-intramol (and on a related note,
> check out http://redmine.gromacs.org/issues/1340).  The nonbonded
> interactions between the coupled molecule and its surroundings are
> affected.  Whether or not intramolecular interactions are affected depends
> on coupl-intramol.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
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-- 



*--------------------Thanks and Regards,Bipin Singh*