[gmx-users] Re: g_rama/xrama problem in version 3.1.4.

[David]

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, 
> 
>   Istvan 
> 
> 
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-- 
David.
________________________________________________________________________
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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