[gmx-users] DNA distortion using oplsaa ff and grompp DNA
David van der Spoel
spoel at xray.bmc.uu.se
Mon Oct 23 21:33:35 CEST 2006
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
> :-) 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
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.
> gmx-users mailing list gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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
More information about the gromacs.org_gmx-users