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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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