[gmx-users] DNA distortion using oplsaa ff and grompp DNA
JLenz at zbh.uni-hamburg.de
Mon Oct 23 16:45:46 CEST 2006
i am trying to find out, why my simulation of a dsDNA molecule gets distorted
after 1.5 ns.
i am using the oplsaa forcefield.
at the very beginning of my simulations i use grompp and got the following
:-) grompp (-:
creating statusfile for 1 node...
# BONDS: 1432
# ANGLES: 2593
# RBDIHS: 3631
# LJ14: 3337
# SETTLE: 24364
# VSITE3: 24364
Analysing residue names:
There are: 24406 OTHER residues
There are: 0 PROTEIN residues
There are: 0 DNA residues
that confuses me a little bit because i have only DNA residues, tip4p water
and NA+ ions in my system.
my question:why does grompp say that there are no DNA residues found. how to
fix this problem ? and can that be the reason for the total distortion of the
DNA after 1.5 ns simulation ? if not, do you have any suggestions for that
thanks a lot in advance
and a happy simulating.
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