[gmx-users] Values for pairs, when attached to the topology...?

Maik Goette mgoette at mpi-bpc.mpg.de
Fri May 13 17:16:32 CEST 2005

Hi Berk

Thanks for the fast answer...

Does this mean, that gromacs recognizes one pair of parameters after the 
2 atom numbers in the pairs section as B-Values, not as A?
For its perhaps easier to script it, am I allowed to enter both A and B 
values after the 2 atom numbers, even if the parameters don't change? 
It's much easier to calculate c6 and c12 out of eps and sig, than to let 
the script attach just the changed parameters, I think.

Hmmm...I don't exactly understand, what the last part means...Does it 
mean, that I am able to include B-parameters via pdb2gmx ?
It only makes sense to me, to change atom types, or create new ones, 
when pdb2gmx is able to do the above...

And for I started questioning....;)
Have the bonded parameters of perturbed atoms to be inserted, when 
nothing on the bonds or angles changes?


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

Berk Hess wrote:
>> From: Maik Goette <mgoette at mpi-bpc.mpg.de>
>> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> To: GMX-mailinglist <gmx-users at gromacs.org>
>> Subject: [gmx-users] Values for pairs, when attached to the topology...?
>> Date: Fri, 13 May 2005 14:49:01 +0200
>> Hi all
>> I have a problem with parameters, manually included to the pairs 
>> section. For FEP purposes, I have(?) to include the pair parameters 
>> for the perturbed atoms ((A and B value) into the topology file 
>> I took the values eps and sig for the two atoms i and j from the 
>> nonbonded topology, calculated the ij value via the formulas in the 
>> manual and inserted these values for eps and sig in the topology file.
>> mdrun claims, that the parameters are wrong:
>> Fatal error: Force field inconsistency: 1-4 interaction parameters for 
>> atoms 1615-1621 not the same as for other atoms with the same atom type
>> Obviously, the parameters, I calculated are wrong. Do I have to 
>> include fudge-factors in my calculations ?
>> I am also not sure, if there have to be c6 and c12 in the topology 
>> file, or if eps and sig are ok.
>> Please give me some information, how the parameters out of the 
>> forcefield have to be calculated correctly and which ones I have to 
>> use in my topology file
> You only need to enter the B-topology parameters when they are
> different from the A values.
> Unfortunately there are two problems in 3.2.1:
> the pair parameters should always be in c6/c12 form
> and you can not have different pair parameters for the same
> atom type combinations.
> Both problems have been fixed in the CVS, but the CVS code
> currently has no free-energy loops.
> But I think that if you only change the charges and/or atom types
> all bonded parameters (including the pairs) should be set
> correctly for the B topology by grompp.
> Berk.
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