[gmx-users] DNA/RNA records for OPLS force field in GROMACS format.

Marc Kreissler m.kreissler at lpcm.u-bordeaux1.fr
Thu Feb 24 12:32:45 CET 2005

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  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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