[gmx-users] Re: g_rama/xrama problem in version 3.1.4.
spoel at xray.bmc.uu.se
Thu Sep 25 19:28:01 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.
> 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
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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