[gmx-users] Is the AMBER or CHARMM Force field running in GROMACS

david.evans at ulsop.ac.uk david.evans at ulsop.ac.uk
Thu Jul 15 12:26:41 CEST 2004


Thanks very much for posting this. Changing the mass of the oxygen in
my tip3p water
from 16.0000 to 15.9994, has enormously slowed the diffusion of the
DNA molecule in my system!
Gromacs appears now to be more consistent with Amber (see my postings
yesterday). I'm doing NVT simulations atm, so I haven't compared the
I can only speculate that the SETTLE algorithm is hugely sensitive to
the masses, but why this would be the case I've no idea. 

Thanks again


---- Message from Michel Cuendet <michel.cuendet at epfl.ch> at
2004-07-15 11:06:58 ------
>You can use Amber ff in gromacs, but be careful with the water.
>water converted with ambconv give very strange results for the
>and can even induce protein tearing apart (see previous postings on
>list). To cure this problem, you have to replace the tip3p masses by
>spc masses in your topology. This strange sensitivity of gromacs to
>water atom masses is still an unsolved problem...
>Michel Cuendet
>Laboratory of Computational Biochemistry and Chemistry
>Institute of Chemical Sciences and Engineering
>Swiss Federal Institute of Technology in Lausanne (EPFL)
>CH-1015 Lausanne						
>Switzerland                         	Phone : +41 1 693 0324
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