Re: [AMBER] PMF calculation

From: somdev pahari <>
Date: Tue, 29 Sep 2020 11:20:19 -0700

Thank you Callum sir for your quick response and detailed explanation.
I forgot that there were two different force fields in the tutorial and in
the publication, that's my bad.
I will definitely try with benzene and will let you know if anything finds

Somdev Pahari

On Mon, Sep 28, 2020 at 1:38 PM Dickson, Callum <>

> Hi Somdev,
> Your results look quite reasonable but you will need to simulate longer to
> get convergence. Why do you think you should have negative values? Debasing
> the results so that dG=0 in the water phase, a negative region would
> indicate methanol prefers the lipid bilayer environment over water.
> If you look at the PMF curve in the tutorial, although it comes back down
> close to zero, at no point is the free energy negative, indicating methanol
> would prefer to remain in water using GAFF and lipid14 force fields. In the
> Orsi paper, it seems like the free energy for methanol is very slightly
> negative around the lipid head group region, however these simulations used
> a coarse grained membrane so it is hard to directly compare.
> The logP for methanol is around logP = -0.5, so it prefers water over oil.
> logP doesn't always track directly with membrane partitioning but it is a
> good indicator. If you run the same PMF for something like benzene (logP ~
> 2), it should certainly prefer the membrane environment with -ve free
> energy.
> Best,
> Callum
> -----Original Message-----
> From: somdev pahari <>
> Sent: Tuesday, September 29, 2020 4:25 AM
> To: AMBER Mailing List <>
> Subject: [AMBER] PMF calculation
> Dear Amber users,
> I am trying to calculate PMF for the lipid membrane system and using this
> tutorial as a reference (
> ) with Amber 18.
> I am trying to reproduce some results as described in the tutorial as well
> as in this paper (
> ), also mentioned in the tutorial.
> I did it for water and methanol. What I faced that in the case of methanol
> there do not have any single negative value as it should be. I took 0.5 A
> as window width and ran a test simulation of 5 ns for each. I know that
> it's not enough for convergence, still, am I missing something? Kindly help
> me out.
> Thanks in advance.
> Regards
> Somdev Pahari
> Research Scholar
> NIT Rourkela
> Odisha, India
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Received on Mon Sep 28 2020 - 23:00:02 PDT
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