[gmx-users] DNA distortion using oplsaa ff and grompp DNA
David van der Spoel
spoel at xray.bmc.uu.se
Tue Oct 24 11:33:24 CEST 2006
Joern Lenz wrote:
>>> dear users,
>>> i am trying to find out, why my simulation of a dsDNA molecule gets
>>> 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
>>> fix this problem ? and can that be the reason for the total distortion of
>>> DNA after 1.5 ns simulation ? if not, do you have any suggestions for that
>> grompp doesn't know what DNA is, but that's not the problem.
>> Did you use enough ions in your simulation and use PME for electrostatics?
> greetings david and thanks for the answer,
> I used genion to include 42 NA+ ions to exactly compensate the negative charge
> of the dsDNA. no more ions are in the system.
> what is the problem with PME and ions ? Should i use PME or not ?
> thanks a lot for your work wiith gromacs
You definitely need PME for systems like this. Did you?
Otherwise, the size of the box might play a minor role.
If all else fails you might want to try the Amber FF.
Are you sure what the conformation of your DNA should be in solution
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
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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