[gmx-users] DNA distortion using oplsaa ff and grompp DNA
JLenz at zbh.uni-hamburg.de
Tue Oct 24 11:13:30 CEST 2006
>> 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
>> thanks a lot in advance
>> and a happy simulating.
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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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