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

david.evans at ulsop.ac.uk david.evans at ulsop.ac.uk
Thu Feb 24 12:58:18 CET 2005


I think that 60 water molecules is far too few. One would typically
add a few thousand in a box extending about 10 angstroms from
the solute.

If it's not too heretical for this list, might I suggest looking 
at the DNA tutorial on the Amber web site? This, and the
cited references, give a good idea of what people do in the
successful DNA simulations to date.

good luck,

>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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