Dr Steinbrecher,
I did not run any test simulation to see whether the dvdl_norest = 1 and 0.
But with your suggestion, I did perform my lambda simulations with
dvdl_norest = 0 and manually subtracted the values of RESTRAINT from DV/DL &
and the values for my free energies are almost equal.
Let me explain:
For single ion mutations, the difference in K+ ---> N0 & Cl- ---> N0, the
deltaG difference = -20.32159 kcal/mol
And for the concurrent dual mutation K+ + N0 ---> N0 + Cl- the deltaG
= -20.2621165 kcal/mol
According the article that I was citing here in the emails, these tests
prove the independent nature of concurrent dual mutation.
I might have a question or two for later, but thank you very much for your
time in helping me solve through this!!
Regards
Sai
On Tue, Jan 31, 2012 at 2:25 AM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> > If I have to manually remove or subtract the restraint contribution from
> > the DVDL,
> > should I use the values printed at the end of the simulation that reads:
> >
> > DV/DL, AVERAGES OVER 500000 STEPS
>
> this should have an entry RESTRAINTS and that is all you need to subtract.
> If I remember correctly, dvdl_norest only changes the reported output, not
> your simulation results. If you want to test my recollection, run a simple
> simulation twice with dvdl_norest on and off and see if the difference in
> dvdl matches the RESTRAINT entry.
>
> Kind Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Tue Jan 31 2012 - 09:30:02 PST
