[gmx-users] Re: g_rama/xrama problem in version 3.1.4.
istvan at kolossvary.hu
istvan at kolossvary.hu
Fri Sep 26 13:32:00 CEST 2003
> On Thu, 2003-09-25 at 15:46, istvan at kolossvary.hu wrote:
>> Hi, David, Erik,
>> Erik Lindahl wrote:
>> > Hi David,
>> >> I suspect it's a force field problem, that is you used OPLS, whereas I'm
>> >> afraid to admit that part of this code expects the topology to have
>> >> gromos-like dihedrals. If this is the case you coud remake a topology
>> >> using the ffgmx2 force field and use that for this analysis only.
>> I did this and it works. I suppose if I change the ACE/NAC atom names for
>> the methyl carbon from CH3 to CA in the OPLS-AA .rtp and .hdb files that
>> would be OK, too. I'll let you know.
>> In the meantime, two quick questions. What is nrexcl in the topology file?
>> There is a reference to this in the manual saying that, e.g., benzene should
>> have a nrexcl=5 in order to exclude all intramolecular contributions to make
>> autocorrelation functions smoother. With my ACE-ALA-NAC nrexcl is set to 3
>> by default. What does it mean?
> This is explained in the manual (chapter 4)
>> My other question is -fee in g_energy. It says G = -kT * ln< e^(E/kT)>. What
>> exactly does < e^(E/kT)> mean? If I sum up ALL of the energy levels of a
>> system that way, it gives the partition function and that is OK. However, if
>> I do sampling (Metropolis MC or MD), I cannot guarantee that I visit all of
>> the energy levels. All I can say is that I can keep detailed balance and
>> sample low-energy states more frequently (exponentially more frequently)
>> than high-energy states. Therefore, the exponential character is already
>> there in the sampling. My concern is that averaging "exponentially"
>> according to < e^(E/kT)> while sampling "exponentially" via MD would somehow
>> "double-exponentiate" the average. I am probably missing something. Could
>> you clarify this.
> This was recently discussed on the mailing list.
Thanks. I checked the correspondence, but it didn't answer my question. I
guess I'll just do a hand calculation from the energy file to figure what
exactly is calculated. I'll report back if I find something interesting,
looks like there is general interest.
>> Many thanks,
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> David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
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