[gmx-users] Free energy in octanol and water
jalemkul at vt.edu
Wed Sep 30 13:33:44 CEST 2015
On 9/30/15 3:13 AM, Gmx QA wrote:
> Hi Justin
> Thanks, that is a good suggestion, I will try that.
> Besides running multiple replicates, is there something else that is
> obviously wrong with my method?
Not that I can see.
> 2015-09-29 19:09 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
>> On 9/29/15 4:51 AM, Gmx QA wrote:
>>> Hi gmx-users
>>> I am trying to calculate the free energy of solvation for a drug-molecule
>>> in octanol and water.
>>> I am comparing two situations:
>>> A: Two systems, one with the drug in water only, and one with the drug in
>>> pure octanol.
>>> B: drug in water only (same as in A), and then one box where I have added
>>> 20% water to my octanol system (since mixtures of octanol and water
>>> typically contains some water in the octanol phase).
>>> Then I run a series of free energy calculations per Justin's tutorial, 48
>>> lambda points in total.
>>> For system A I get a Delta-G for pure water of 39.07 kJ/mol, and 92.81
>>> kJ/mol in pure octanol.
>>> For system B, the Delta-G for pure water is the same, but for the
>>> octanol-box with 20% water the Delta-G is 95.99 kJ/mol.
>>> All of these results are obtained using gmx bar in gromacs 5.0.4.
>>> My main concern is that the Delta-G is higher in the water/octanol mixture
>>> than in pure octanol, but I would have expected the reverse to be the
>> From experience, I can tell you it is very hard to get good convergence on
>> such mixtures. You'll note that in npt.gro you effectively have two bands
>> of water formed in the box, neither or which is particularly close to the
>> API molecule. You'll probably get some microscopic phase separation. The
>> route I've gone in the past is to generate several starting configurations
>> (different random seeds when inserting the water molecules) and averaging
>> over multiple runs. You should also do some error analysis of your results
>> (both block averaging for convergence, and to compare the two DG values
>> between the systems). Without error bars, you have no idea if those two
>> values are at all meaningfully different.
>> Is there something wrong with my protocol? The forcefield is
>>> GAFF/amber99sb,and all production runs are 10 ns in length.
>>> I have uploaded copies of all input-files here:
>> 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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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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