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

[Andrey V. Golovin]

Dear Marc.
Dave right. DNA keeps structure mainly by hydrofobics.
So no water no hydrofobicity. Please use: genbox -cs
to get anought water. Good luck. 

P.S. And please renew forcefiled files, we added there 3' and 5' end residues. 
you can get it from my page (http://rnp-group.genebee.msu.su/3d/oplsa_ff.html)
and soon in contribution page.
----
Best regards, Andrey
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Andrey V. Golovin
Ph.D,Professor assistant    tel: +7 (095) 939-5305  
Bioengineering and
Bioinformatics Department              
Moscow State University     fax: +7 (095) 939-3181
119899 Moscow            E-mail: golovin at genebee.msu.su
Russia                      web: http://rnp-group.genebee.msu.su
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---------- Original Message -----------
From: Marc Kreissler <m.kreissler at lpcm.u-bordeaux1.fr>
To: Andrey V Golovin <golovin at genebee.msu.su>, Discussion list for GROMACS
users <gmx-users at gromacs.org>
Sent: Thu, 24 Feb 2005 12:32:45 +0100
Subject: Re: [gmx-users] DNA/RNA records for OPLS force field in GROMACS format.

> Andrey V Golovin a &eacute;crit:
> 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 excessnegative
> charges due to phosphate groups.
> 
> i get a surprising result after 1ns of simulation ( about 3hourson a 
> Linux_PC) :
> 
> the double-helix ends up in a dissociated state.
> 
> for this calculation i use - a triclinic box
> - pme forelectrostatics
> - 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 thissystem ?
> - and last but not least i don't know if the periodic 
> boundaryconditions are on or off ?
> 
> a lot of questions.
> 
> i would appreciate your helpfull advices.
> 
> merci , cordialement
> 
> marc kreissler
------- End of Original Message -------