Re: FEP tutorial graph question

From: Christopher Hartshorn (
Date: Fri May 01 2009 - 12:05:21 CDT

Chris and Jerome,
Thank you again for the journal links, etc. So, I reran the tutorial
with the new parameters in 2.7 and the pllot "looked" better, but
nothing like the 2.6 type from tutorial. I then reran using NAMD2.6
and got exactly the same graph as in the tutorial (nice smooth
increase up to 20kcal/mol then sharrp/smooth drop near the end. I
guess this was to be expected because of the lack of the soft-core
approach in 2.6. So, I have three questions this time.

1) Besides the fact that the softcore approach is tunable, what are
the other advantages over the old? Is it computational cost or more
realistic, etc.

2) Since the latest 2.7 is so much faster (150%) on all of my systems
I would, of course, prefer to keep using it. What config file lines
would I put to start an FEP calculation in 2.7 that ran exactly the
same as 2.6 to test that extreme (e.g. softcore off) versus others
with softcore on? Would this just be "decouple off?"

3) Since these runs can take up to 25 days each, which parameters
would be best to change first in order to minimize the amount of runs
I would need to find the ideal set of softcore parameters? In other
words, what if anything would make me want to change, hypothetically,
fepElecLambdaStart 0.5 to fepElecLambdaStart 0.3 or fepVdwLambdaEnd
1.0 to fepVdwLambdaEnd 0.8 etc. etc. after looking at a plot of dG vs.
lambda step?

Thank you very much. I know I have a lot of questions. So, hopefully
they will be a benefit to others as well.



On May 1, 2009, at 6:35 AM, Chris Harrison wrote:

> Chris,
> I just wanted to quickly let you know I got your email and will send
> a more complete answer later today. However, I did want to mention
> that the plot you got looked not dissimilar to plots we got during
> early stages of implementing softcore, so it may not be as bad as
> you feared and only require the proper softcore parameters. The
> tutorial is still based on FEP in NAMD2.6; we are currently working
> on an updated tutorial that will released shortly after the official
> NAMD2.7 release. Please let me know how the run using the parameters
> I sent turns out, as this will be a strong indicator to me if there
> is a bug. I'll send a more complete answer to your question(s)
> later today.
> C.
> --
> Chris Harrison, Ph.D.
> Theoretical and Computational Biophysics Group
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
> Voice: 217-244-1733
> Fax: 217-244-6078
> On Thu, Apr 30, 2009 at 12:57 PM, Christopher Hartshorn <
> > wrote:
> Chris,
> Thank you for the help. Much appreciated. As far as the plot I
> have attached the graph to this email. I can not send it to the
> server.
> As far as what I am plotting on this graph, I am plotting up the end
> line of every Lambda step (which is at every 10000th line in
> my .fepout file because I am doing 100Ksteps which are output every
> 10) which includes the overall dG (which I am assuming is the sum
> of all dG's for each Lambda step up to that point) up to that
> point. Not the n-iterations for each. I do separately plot each
> set of n-iterations for each lambda step to verify if it has
> converged (e.g. become relatively constant for a long period of time
> or n-steps). I guess my question is does the plot seem normal and
> if it is why would it be so far off of all the others I see out
> including the one in the tutorial for the exact same simulation/
> calculation?
> In this case where I ran the tutorial and got the attached plot of
> dG vs. lambda (which looks nothing like the plot in the tutorial), I
> did exactly as is told for mutation in a water box with about 20
> lambda steps each of which go for 100000 steps (or 100ps). I have
> verified that it having "converged" for each step. I am running the
> exact same tutorial right now with the three extra lines you mention
> at the beginning of your email to see if anything changes. Ill let
> you know when done if it works for me.
> Finally, is "doubly-decoupled" the same or something different then
> a "double-annihilation?"
> Best,
> Chris
> On Apr 30, 2009, at 8:23 AM, Chris Harrison wrote:
> fepElecLambdaStart 0.5
> fepVdwLambdaEnd 1.0
> decouple on

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