Re: Alchemical FEP NAMD tutorial - problems with reproducing the results

From: Chris Chipot (
Date: Thu Feb 21 2008 - 03:19:42 CST

Dear Jawahar,

please, check the convergence of your simulation in each window.
In particular, pay attention to possible end-point catastrophe
when lambda approaches either 0 or 1.

Chris Chipot

Jawahar Neelankatan a écrit :
> Hi Chris,
> Thank you very much for your email. I was able to use psfgen with the
> correct patches (ACE at N-terminal and CT3 at C-terminal) to generate
> the correct structure. I used this structure to do a simulation (in
> vacuo) using the same parameters listed in the tutorial (300K, 10 ps^-1
> damping coefficient, cutoff electrostatics, rigidBonds set to 'all', and
> integration timestep of 0.5 fs) however I got a dG of 3.97 kcal/mole as
> opposed to the value of 4.4 kcal/mole reported in the tutorial.
> I suspect the reason for this discrepancy might be that the initial
> coordinates and velocities of my system differ from that used in the
> tutorial. Is there a long enough simulation (longer than 2.5 ns) I can
> do that would more closely approximate the tutorial's results ? Also, I
> noticed the huge temperature fluctuations even though I used the
> relatively high damping coefficient of 10 ps^-1 (as instructed in the
> tutorial).
> Thanks again for your email.
> -Jawahar


Chris Chipot, Ph.D.
Equipe de dynamique des assemblages membranaires
Unité mixte de recherche CNRS/UHP No 7565
Nancy Université Phone: +33 (0)3-83-68-40-97
B.P. 239 Fax: +33 (0)3-83-68-43-87
54506 Vandœuvre-lès-Nancy Cedex


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