[gmx-users] Free Energy Topology between A and B.

Nash, Anthony a.nash at ucl.ac.uk
Mon May 30 00:28:49 CEST 2016

So there is! Many thanks for bringing this to my attention.


On 29/05/2016 20:40, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
behalf of Justin Lemkul"
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
jalemkul at vt.edu> wrote:

>On 5/29/16 3:37 PM, Nash, Anthony wrote:
>> Dear all,
>> I¹m a total newbie when it comes to Thermodynamic Integration, and until
>> now I¹ve been happy with umbrella sampling. However, I¹ve found myself
>> a situation where I believe TI would be the most appropriate technique.
>> I would like to determine the energetic contribution that a mutant amino
>> acid has to a protein-protein interaction. The structure is very
>> so pulling along a reaction pathway is out of the question, thus an
>> alchemical path might work.
>> I wish to integrate from state A to state B. The number of atoms in the
>> wild type amino acid of state A are fewer that those in the mutant amino
>> acid of state B. The example given in section 5.7.4 of the manual
>> demonstrate integrating from propanol to pentane, but due to the
>> FF each topology shares the same number of atoms. Atom PC2 and PC3 of
>> state A does not require redefining in typeB chargeB and massB, they are
>> transferred across as they are in both structures. How does one define a
>> mixed A B topology when the number of atoms differ? I.e., if those two
>> atoms in the above example were not needed in state B.
>You need to define transformations between dummy and real atoms.  Look
>into the 
>pmx program (this was mentioned on the list just the other day for an
>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
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