[gmx-users] Re: non-symmetric matrix and too large first values--my mdp files

[Bert de Groot]

medeawan at sohu.com wrote:

[...]

> Are they OK?

yes the mdp files look ok (ie no constraints, no pbc and infinite cutoff)
are you using the vacuum forcefield? Otherwise you may want to use a
different epsilon_r than the default of one (especially with the large
explicit charges on the DNA).

> And another question, you said
> "If this is really caused by the choice of the dihedral
> parameter, then it's no use calculating further until you found the proper
> (+consistent+complete) forcefield parameters."
> Do you mean to do EM and NMA for DNA, what I did including add H and change
> atom names in (bond, angle and dihedrals part in) .rtp file is not enough?
> Then what should I do? Although, I know the GROMOS96 forcefield not support DNA
> simulation well(from the users-archives before), but it's the only software I
> can get now.
> 

I'm no DNA expert, but apparently there are some issues with the forcefield you
used. The first question to clear is now what causes your problem: the algorithm 
or the force field. From tests on peptides and small proteins I tend to trust
the software, but then again the last time I used NMA was with gmx1.6 or 2.0,
so I don't know for sure about newer versions. So please first check the force field:
do the structures after EM look ok? (ie no large deviations from the start
structure, no weird geometries?); does the structure behave ok in a short MD simulation?

Once this is cleared, and still the problems persist, then it's time to test
exactly the same procedure on a peptide/small protein (preferably one for
which there are literature values to compare with. bpti?). 



Bert

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
____________________________________________________________________________