[gmx-users] DNA/RNA records for OPLS force field in GROMACS format.
mgoette at mpi-bpc.mpg.de
Fri Feb 25 10:30:35 CET 2005
I would suggest editconf -d 1
That means 10A distance DNA/Box. That should be enough space and works
fine in my protein/DNA system.
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Marc Kreissler wrote:
> Andrey V Golovin a écrit:
>>We added RNA/DNA entries to OPLS-AA/L force field.
>>If you interested please look at :
>>Some info about testing and building of the records you can found at:
>>PLEASE take in account that it is alpha-alpha version. Some additional
>>testing is needed AND careful compassion with the literature is needed
> bonjour andrey,
> after some work and many "try and error" i have succeeded to
> build the various files which are necessary for running Gromacs
> calculations on a DNA_decamer with about *60 water molecules*,
> *2 Ca++ ions* and *15 Na+ ions* to neutralise the excess negative
> charges due to phosphate groups.
> i get a surprising result after 1ns of simulation ( about 3hours on
> a Linux_PC) :
> the double-helix ends up in a dissociated state.
> for this calculation i use - a *triclinic box*
> - *pme* for electrostatics
> - T_coupling at *300K*
> - *no* P_coupling
> - *oplsaar* force field
> my experience in MD_simulations is not tremendous, especially
> concerning the simulation parameters.
> - i am wondering if i have choosen the *right box form* ?
> - what about the *box dimensions* ?
> - may be the number of water molecules is *too small* for this system ?
> - and last but not least i don't know if the *periodic boundary
> are on or off ?
> a lot of questions.
> i would appreciate your helpfull advices.
> merci , cordialement
> marc kreissler
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