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

[David van der Spoel]

Joern Lenz wrote:
>>> 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
> 
> 

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 
however?

-- 
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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