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

[istvan at kolossvary.hu]

Hi David, 

David wrote: 

> 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)

Thanks. 


>> 
>> 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,  
>> 
>>   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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