Hi David,
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
other interface?
Thanks,
Jagannath
On Apr 12, 2007, at 5:06 PM, David van der Spoel wrote:
Jagannath Mondal wrote:
Hi,
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
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.
______________________________________________________________________
__
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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