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

[Hugo Verli]

Dear Joern,

we also have found problems in simulating DNA with OPLSA, i.e. the base pairing
is broken. Such behaviour is observed only after several nanoseconds (we
performed PME simulations of a dsDNA for 30ns) and is not reversed in the
simulation.

By using the AMBER ports for GROMACS you circumvent this problem.

http://folding.stanford.edu/ffamber/

Best regards,

Hugo Verli.

Citando Joern Lenz <JLenz at zbh.uni-hamburg.de>:

> >> 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
> >> output:
> >>
> >>                                   :-)   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
> >> distortion?
>
>
> >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
> joern
>
>
>
> >> thanks a lot in advance
> >> and a happy simulating.
> >> joe
> >> _______________________________________________
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>
>
>
> -- David.
> ________________________________________________________________________
> 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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Prof. Hugo Verli
Departamento de Produção de Matéria Prima
Faculdade de Farmácia - UFRGS
Av. Ipiranga 2752, Porto Alere, RS
CEP 90610-000, Brasil
tel.: +55 51 3316 7770
      +55 51 3316 5526

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