[gmx-users] topology treatment in free energy calculations -possible bug

[Maik Goette]

Berk

Thanks for the clarification.

I was aware of A-values copied to B-values, when no B-values in the FF 
exist, but actually this was new to me.

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Berk Hess wrote:
> This behavior is itentional.
> But it can indeed be confusing.
> Therefore in Gromacs 4.0 a warning will be generated (and I have added
> a table in the manual that explains all the possible combinations).
> 
> If you explicitly define parameters for the A-state, I don't see why
> you would want the B-parameters to be looked up based on atom-type.
> You would only want that when the A-state parameters are also determined
> by the atom type.
> 
> Berk.
> 
> 
>> 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] topology treatment in free energy calculations 
>> -possible bug
>> Date: Fri, 04 Jan 2008 15:15:57 +0100
>>
>> Hi
>>
>> I just found a strange behaviour of GROMACS, when processing 
>> topologies with B-values. Maybe I just think of it as unintuitive/bug, 
>> but here we go:
>>
>> e.g. OPLS
>>
>> Consider an angle given (all atoms have B-values, which 
>> angle-parameter can be found by GROMACS in the bonded.itp for the A- 
>> and B-state):
>>
>> Original topology entry:
>> 10    12    14     1
>>
>> Manually edited entry (with the correct ff-term):
>> 10    12    14     1     109.700     669.440
>>
>> Now, a dump from the tpr-files yields the following:
>> Original:
>> functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 
>> 1.09500e+02, ctB= 2.92880e+02
>>
>> Edited:
>> functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 
>> 1.09700e+02, ctB= 6.69440e+02
>>
>> Now, what obviously happens is, that GROMACS searches the entries of 
>> the angle in the FF for both states and uses them in the case of the 
>> original topology.
>> If one puts a manual entry into the topology for the A-state though, 
>> the B-state is simply copied, instead of searched by GROMACS.
>>
>> This, IMHO, is quite inconvenient. Is this a bug or a feature?
>>
>> Regards
>>
>> -- 
>> Maik Goette, Dipl. Biol.
>> Max Planck Institute for Biophysical Chemistry
>> Theoretical & computational biophysics department
>> Am Fassberg 11
>> 37077 Goettingen
>> Germany
>> Tel.  : ++49 551 201 2310
>> Fax   : ++49 551 201 2302
>> Email : mgoette[at]mpi-bpc.mpg.de
>>         mgoette2[at]gwdg.de
>> WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/
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