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

[Joern Lenz]

>> 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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