[gmx-users] Ace-Ala-Nac to Ace-Gly-Nac

David Mobley dmobley at gmail.com
Sat Nov 10 23:30:19 CET 2007

Dear Bharat,

OK, I went ahead and ran with your topologies using my own run
scripts. My runs haven't finished yet,  but looking at just
<dV/dlambda> values from equilibration,  I seem to be seeing roughly
the same trends you do. In particular:
(1) The forward simulation always gives dv/dlambda values that are
fairly close to -2 at each lambda
(2) The reverse simulation gives a range of <dv/dlambda> values at
different lambda values, and switches from positive to negative as
lambda increases.

The integral of <dV/dlambda> in the forward case is NOT the negative
of the integral of <dV/dlambda> for the reverse case, which is what it
should be.

Obviously, something is wrong here, and it doesn't seem to be your run
input files. I don't see anything obviously wrong with your topology
files, either -- as far as I can tell your charge groups are OK.

My suggestion is to try to strip this down to a simpler case where it
will become more clear what the problem is. Maybe ethane->methane
rather than with the capping on the ends.  (Did you say you have the
same problem with ethane->methane? It would be easier to troubleshoot
those topologies).

If you get to the point where you're convinced it has nothing to do
with your topology, you could submit a bugzilla -- but it would be a
good idea to be more sure that there is no problem with your topology,
first. Also it would be helpful to have more evidence about where the
bug might be, if there is one (hence the importance of stripping this
down to the "minimum" topology necessary to reproduce the problem).

You might also, for example, just try turning off the charges on
methane in water. You could also try turning on the charges in methane
in water. These two should be equivalent (except for the sign) of

Keep me posted on what you find out.


Hope that helps. Keep me posted on what you find.

On Nov 7, 2007 10:42 PM, bharat v. adkar <bharat at sscu.iisc.ernet.in> wrote:
> Hi David,
> This is regarding our discussion on gromacs mailing list on "soft-core
> and coulomb transformation". Sorry for delay in reply. I am  attaching a
> TGZ file which contains a script to run the simulations and a MDP folder
> with all required files.
> The system is Ace-Ala-Nac, i.e., alanine capped at both ends.
> The MDP files are made to run the FORWARD simulations, i.e., from
> alanine->glycine. To run the REVERSE simulations, in all MDP files,
> "define = -DFE_coul_rev" has to be defined.
> I am sorry for a lot of botherance. but i am not getting the same values,
> within error limit, as i mentioned in the mailing list. I will send my set
> of values to you most probably by tomorrow.
> Thanks.
> bharat
> --
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