From: Brian Radak (bradak_at_anl.gov)
Date: Mon Jan 09 2017 - 10:11:47 CST
I would check the citation for the force field parameters. Almost all
ion parameters published in the literature come with either absolute or
relative solvation free energy numbers. The standard CHARMM36 prm file
actually states that the value should be -18.6 kcal/mol.
If you cannot reproduce those numbers with NAMD, then I might be
concerned, especially if NAMD (or maybe CHARMM) was used for the
On 01/09/2017 01:55 AM, Hannes Loeffler wrote:
> You had and answer to your question just recently although the numbers
> seem to be different. I think what you need to do is to engage in a
> discussion to get an answer to your question rather than just repeat
> your question a third time. In particular you would need to give at
> least some detail as to what you have done. Otherwise it will be
> difficult to find out where the problem is ... if there is any.
> Your result appears to be quite ok compared to the one you cite. That
> simple system must have been computed many times over and it is
> certainly not enough to compare to just one source. So you probably
> should look for other literature and get a feel how different such free
> energies can be. Some reasons have been pointed out by the other
> poster, e.g. force field. I would expect ions to be quite sensitive to
> On Mon, 9 Jan 2017 11:39:32 +0530
> Abhishek Kumar Singh <ar3406_at_gmail.com> wrote:
>> Dear all,
>> I'm alchemically transforming K+ into Na+ in a water box using
>> CHARMM36 force field. I got the solvation free energy difference
>> between K+ and Na+ -23.40 Kcal/mol while in one research publication
>> (VB Luzhkov et al. Biochim Biophys Acta 1548 (2), 194-202. 2001 Aug
>> 13) they have shown -17.33 Kcal/mol solvation free energy difference
>> between K+ and Na+ using programme Q with GROMOS 87 force field.
>> What can be the reason of this difference ?
>> I appreciate your suggestions.
-- Brian Radak Postdoctoral Appointee Leadership Computing Facility Argonne National Laboratory 9700 South Cass Avenue, Bldg. 240 Argonne, IL 60439-4854 (630) 252-8643 brian.radak_at_anl.gov
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