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

[Xavier Periole]

On Fri, 5 Sep 2008 09:48:38 -0500
  "NAMD GROMACS" <namd.gromacs at gmail.com> wrote:
> 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.
the manual is online on the gromacs page and you can download the paper
version (pdf). in the documentation section of the website
wiki:
http://wiki.gromacs.org/index.php/Main_Page (first result typing "wiki 
gromacs"
in google)
> 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
>> -----------------------------------------------------
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-----------------------------------------------------
XAvier Periole - PhD

Molecular Dynamics Group / NMR and Computation
University of Groningen
The Netherlands
-----------------------------------------------------