Should also have checked my sources first. Scuziscuziscuzi...
Tsjerk
On 6/21/06,
Isabella Daidone <[EMAIL PROTECTED]> wrote:
Thanks Tsjerk,
but what about the following gromacs page:
http://www.gromacs.org/blogcategory/page_4.html
and the following article of van Gunsteren
"J Comp Chem, 1998, 19:535" which suggests the use of 1.4 nm?
Thanks
Isabella
On Wed, 21 Jun 2006, Tsjerk Wassenaar wrote:
> Hi Isabella,
>
> The Gromos force fields were parameterized for use with a rvdw cutoff of 0.9.
> Other cutoffs may introduce artefacts.
>
> Ciao!
>
> Tsjerk
>
> On 6/21/06, Isabella Daidone <[EMAIL PROTECTED]> wrote:
>>
>> Sorry, but I'm a little bit confused about what rvdw to use for
>> simulations of proteins in solution with gromos96 force field while using
>> pme for
>> coulomb interactions.
>> In the gromacs 3.3 manual I still read (with pme):
>> rcoulomb=rlist=rvdw=0.9 nm
>>
>> Then, I found in the discussion list (+ the paper J Comp Chem,
>> 1998, 19:535) someone suggesting rvdw= 1.4 nm.
>>
>> Could you please help me? what's your suggestion?
>> Is it nowadays anyway accepted to
>> use rcoulomb=rlist=rvdw=0.9 nm?
>> And is there any difference between the standard G43a1 version or the
>> newest (G53a...)?
>>
>> Thank you very much.
>>
>> Isabella
>>
>>
>>
>> _______________________________________________
>> gmx-users mailing list gmx-users@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 [EMAIL PROTECTED].
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
>
>
> --
>
> Tsjerk A. Wassenaar, M.Sc.
> Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
> Dept. of Biophysical Chemistry
> University of Groningen
> Nijenborgh 4
> 9747AG Groningen, The Netherlands
> +31 50 363 4336
>
_______________________________________________
gmx-users mailing list gmx-users@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 [EMAIL PROTECTED].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
_______________________________________________ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
