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

[Marc Kreissler]

Maik Goette a écrit:

> Hi
>
> 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.
>
> Regards
>
> Maik Goette, Dipl. Biol.
> Max Planck Institute for Biophysical Chemistry
> Theoretical & computational biophysics department
> Am Fassberg 11
> 37077 Goettingen
> Germany
> Tel.  : ++49 551 201 2310
> Fax   : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.de
>         mgoette2[at]gwdg.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 :
>>> http://www.gromacs.org/topologies/force_fields.php
>>> Some info about testing and building of the records you can found at:
>>> http://rnp-group.genebee.msu.su/3d/oplsa_ff.html
>>>
>>> PLEASE take in account that it is alpha-alpha version. Some additional
>>> testing is needed AND careful compassion with the literature is needed
>>> also.
>>>
>>>  
>>>
>> 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 
>> conditions*
>> 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.

cordialement,
marc kreissler