Alchemical FEP NAMD tutorial - problems with reproducing the results

From: Jawahar Neelankatan (
Date: Mon Feb 18 2008 - 21:25:54 CST

Hi all,
I have a question about the second computational example in the alchemical FEP tutorial available from the NAMD website ( ). This example illustrates how to use FEP to compute the change in solvation Gibbs free energy that occurs upon mutating a short Ala-Tyr-Ala oligopeptide chain to Ala-Ala-Ala. I tried to duplicate the results obtained in the tutorial by following the instructions laid out therein, but I obtained different results. I experienced some issues over the course of the calculation that I would really appreciate some clarification on (from anyone who has followed the instructions and has been able to reproduce the results given in the tutorial), I have listed them below:

(1) Setup phase:
The Alchemical FEP tutorial includes some setup files, e.g. a topology file containing the hybrid topology of tyrosine and alanine ( and the hybrid structure of the whole system (tyr2ala.pdb) The first thing I noticed about the tyr2ala.pdb file is the strange atoms of the first and last alanines. I'm referring to non-traditional atoms going by names such as 'CAY', 'CY', 'OY', 'HY1', etc. Alanine has only 3 carbons but the alanines in tyr2ala.pdb had 5. I also noticed that the topology file included in the setup files ( does not support this odd version of alanine, and, when this topology file is used with psfgen to generate a psf file (using the setup.pgn script given in the tutorial), psfgen basically just complains that it cannot recognize these non-traditional atoms, so it generates the usual alanine. So the alanines generated by psfgen were different (in the number and nature of atoms) from the alanines in tyr2ala.pdb. It was that
 psfgen-generated structure that I used to do my simulations, and I got very different results.

(2) For the vacuo simulation of Ala-Tyr-Ala, I used the parameters listed in the tutorial and did a minimization and short heating initially, before even doing any FEP runs. I noticed that the heating step produced strange results. I used langevintemp to heat up the system slowly in 2K increments from 0K to 300K. The temperature was never stable, and fluctuated widely no matter how slow I heated it, in fact, after heating up to 300K and letting it equilibrate for 20 ps, I was still seeing temperature fluctuations as huge as 150K. I experimented with all sorts of heating times and heating increments and I still couldn't get rid of the wild temperature fluctuations so I gave up and decided to move to the FEP phase of the simulation. I used the .vel, .xsc and .coor files from the minimization and heating run as the starting configuration of the FEP run. I ran the FEP run exactly as specified in the tutorial but the result I got for the free energy difference for the isolated
 (in vacuo) state 3.6 kcal/mol, which is different from the value of 4.4 kcal/mol obtained in the tutorial.

Has anyone else tried to replicate this example by following the instructions in the tutorial ? And if so, were you able to reproduce the values obtained in the tutorial ? Thanks for your help. I've attached the tyr2ala.pdb file that came with the tutorial, so could anyone please explain where to find a topology file that supports the non-traditional atoms ('CAY', 'CY', 'OY', etc.) that the alanines in this pdb file have ? Thanks.


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