[gmx-users] DNA/RNA records for OPLS force field in GROMACS format.
m.kreissler at lpcm.u-bordeaux1.fr
Thu Feb 24 12:32:45 CET 2005
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
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
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