[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?


> 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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