Hi ALL,
I want to do a MD simulation of a GPCR protein using GROMACS vacuum force
field. I want to use the old force field G43b1 (vacuum simulation)
which is not there in GROMACS4.0.3. I would like to know which is the
substitute for this G43b1 force field
from the present menu:
Select the Force Field:
0: GROMOS96 43a1 force field
1: GROMOS96 43a2 force field (improved alkane dihedrals)
2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
6: [DEPRECATED] Gromacs force field (see manual)
7: [DEPRECATED] Gromacs force field with hydrogens for NMR
8: Encad all-atom force field, using scaled-down vacuum charges
9: Encad all-atom force field, using full solvent charges
Should I use the 8th one? The new manual for GROMACS4.0 also does not reflect
this change.
Any suggestion is welcome.
Regards,
Anirban Ghosh
Grade Based Engineer
Bioinformatics Team
Centre for Development of Advanced Computing (C-DAC)
Pune, India
Bollywood news, movie reviews, film trailers and more! Go to
http://in.movies.yahoo.com/_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
