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

Bert de Groot bgroot at gwdg.de
Fri May 16 11:13:01 CEST 2003

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?). 


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

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