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

[Marc Kreissler]

david.evans at ulsop.ac.uk a écrit:

>Hi,
>
>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,
>
>Dave
>-
>  
>
>>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
>>    
>>
>conditions 
>  
>
>>are on or off ?
>>
>>a lot of questions.
>>
>>i would  appreciate your  helpfull  advices.
>>
>>merci ,  cordialement
>>
>>marc kreissler
>>
>>
>>
>>
>>
>>
>>
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>>
>>    
>>
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bonsoir david evans,

thank's for the usefull hint to have a look at the "DNA tutorial"
located on the Amber website. "keep on learning, learning,..." ( a quote 
from vladimir
illitch lenin).

cordialement,
marc kreissler


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