[gmx-users] DNA/RNA records for OPLS force field in GROMACS format.
m.kreissler at lpcm.u-bordeaux1.fr
Fri Mar 4 19:02:54 CET 2005
Maik Goette a écrit:
> 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
> 37077 Goettingen
> 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:
>>> Dear All!
>>> 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
>> 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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bonsoir maik goette,
i am a bit late, but i wanted to thank you for your helpfull
advice with the waterbox dimension .
it works fine.
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