[gmx-users] News on implicit solvent implementation(s) ?

Marc Baaden baaden at smplinux.de
Sat Jun 28 11:22:01 CEST 2003

Hi Erik,

thanks a lot for these very encouraging news and for the continuing efforts on 
Gromacs development.

>> Gromacs4 isn't really suitable for testing right now, since things are 
>> still undergoing major changes, but yes - I have GB loops, and they 
>> will be _extremely fast_.

How did you do it ? I mean is there a similar thing like mkinl for GB ?
Or is it intermixed with the inner loops ?

>> The main work remaining to be done for GB is parameterizing all force 
>> fields, and we have to decide the two best methods for updating the 
>> radii (it will probably be ACE in addition to Still).

OK. How about using the amber forcefield, for which there is a GB 
parametrization and a (not yet official or thoroughly tested ?) implementation 
in Gromacs ?


 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden at smplinux.de      -      http://www.marc-baaden.de
 FAX: +49 697912 39550  -  Tel: +33 15841 5176 ou +33 609 843217

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