[gmx-users] DNA distortion using oplsaa ff and grompp DNA

Joern Lenz JLenz at zbh.uni-hamburg.de
Mon Oct 23 16:45:46 CEST 2006

dear users,
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...
calling /usr/bin/cpp...
processing topology...
#      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
Analysing Other...

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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