[gmx-users] what are the options for implicit solvent in Gromacs?
jmondal at chem.wisc.edu
Fri Apr 13 00:25:43 CEST 2007
Thanks for your email. But then what is the purpose of
option like gb_algorithm, nstgbradii =1 etc.
Is there any way I can do implicit solvent simulation using any
On Apr 12, 2007, at 5:06 PM, David van der Spoel wrote:
> Jagannath Mondal wrote:
>> I am trying to learn how to use implicit solvent model for
>> PMF calculation. For that ,I wanted to know what are the options
>> for implicit solvent present in gromacs. But I could not find any
>> documentation regarding that. I searched mailing list and found
>> that there has been some query on the documentation but I could
>> not find any suitable reply. In one of the reply, David suggested
>> using following command:
>> touch grompp
>> But it does not show all the available option for implicit
>> solvent model gromacs has got. it shows implicit solvent= no.
>> There were some older mail (before 2006) where it was said
>> that gromacs has not gor implicit solvent model. But I hope that
>> latest version has got implicit solvent model. Can anyone suggest
>> any documentation where I can find the availble options for
>> implicit solvent model as well as the other options for
>> Generalized Born model?
>> Thanks in advance,,
>> Yours sincerely,
> sorry. no implicit solvent.
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> David van der Spoel, PhD, Assoc. 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://folding.bmc.uu.se
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