[gmx-users] questions regarding forcefields and .top file

[NAMD GROMACS]

Hi,

Can someone please provide me the link? I couldnt find the link in gromacs
webpage related to these.also in wiki, this is not clearly described.

On Fri, Sep 5, 2008 at 2:47 AM, Xavier Periole <X.Periole at rug.nl> wrote:

> On Thu, 4 Sep 2008 23:22:35 -0500
>  "NAMD GROMACS" <namd.gromacs at gmail.com> wrote:
>
>> Hi,
>>
>> I have a couple of questions regarding top file and forcefield.
>>
>> 1st, in the top file
>>
>> [ angles ]
>> ;  ai    aj    ak funct            c0            c1            c2
>> c3
>>   2     1     3     2    ga_9
>>   2     1     4     2    ga_9
>>   2     1     5     2    ga_10
>>   3     1     4     2    ga_9
>>   3     1     5     2    ga_10
>> Can you please tell me what the word "funct: stands for? what kind of
>> functionals, why the numbers 2, and then in case of angles it changes to
>> 1?
>> I couldnt find good explanation for this in any manual or tutorial.
>>
> there is chapter dedicted to this ... and there the wiki (link at
> www.gromacs.org) ...
>
> Also what does ga_9, ga_10 etc means..I guess the a in ga stands for angle,
>> I dont know where the g is coming from. I am guessing the numbers are
>> different types of bond.
>>
> you should have a look at the paper of the force field.
>
>>
>> Question regarding the force-field.
>>
>> Select the Force Field:
>> 0: GROMOS96 43a1 force field
>> 1: GROMOS96 43b1 vacuum force field
>> 2: GROMOS96 43a2 force field (improved alkane dihedrals)
>> 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
>> 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
>> 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>> 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>> 7: [DEPRECATED] Gromacs force field (see manual)
>> 8: [DEPRECATED] Gromacs force field with hydrogens for NMR
>> 9: Encad all-atom force field, using scaled-down vacuum charges
>> 10: Encad all-atom force field, using full solvent charges
>>
>> Here I am choosing 2 for my peptide in water run. I am wondering If I need
>> to study peptide-mineral surface interaction, what number should I chose?
>> Is
>> there a way I can go beyond 10, or can I dvelop my own force field, .top
>> file for interacting with mineral surface? Any suggestions on how to
>> develop
>> new .top file including metals and metal oxide surfaces would be also
>> great
>> help.
>>
>> Thanks
>>
>> Subhashis
>>
>
> -----------------------------------------------------
> XAvier Periole - PhD
>
> Molecular Dynamics Group / NMR and Computation
> University of Groningen
> The Netherlands
> -----------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080905/f3ffbd63/attachment.html>