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

[Maik Goette]

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
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.