[gmx-users] custom forcefields or a new forcefields
gareth.tribello at gmail.com
Thu Apr 1 15:28:32 CEST 2010
Oh almost forgot you also have to put
vdw-type = user
in the mdp file. As this tell gromacs to read in the tables.
On Thu, Apr 1, 2010 at 3:25 PM, Gareth Tribello
<gareth.tribello at gmail.com>wrote:
> Basically you can provide a file in which you calculate the values of your
> potential function for different values of r. You will have to write a
> small program to create the table file yourself I think. The details of
> what should be in it are described in section 6.7.2 of the manual but
> briefly gromacs treats your forcefield as follows:
> V(r) = (q_i q_j / 4 pi eps_0 ) f(r) + A g(r) + C h(r)
> Your table should have seven columns which are:
> r, f(r) , f'(r) , g(r), g'(r) , h(r), h'(r)
> Gromacs will then get itself the A and C from the topol.top file.
> (incidentally your mix type in the initial defaults line should be 1). The
> spacing between r values will depend on whether you are using a single or
> double precision version of gromacs.
> As an example if you were using Lennard Jones with a coulomb interaction
> f(r) = 1/r
> g(r) = -1/r**6
> h(r) = 1/r**12
> You then need to put the tables you are using in the directory in which you
> are running gromacs.
> On Thu, Apr 1, 2010 at 12:08 PM, DreamCatcher <huangshuping1987 at gmail.com>wrote:
>> Message: 5
>> Date: Thu, 01 Apr 2010 16:30:44 +1100
>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>> Subject: Re: [gmx-users] custom forcefields or a new forcefields
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <4BB42F84.9050703 at anu.edu.au>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> On 01/04/10 16:20, DreamCatcher wrote:
>> > Hello gmx-users,
>> > I have just look through the mail-list to find this
>> > http://lists.gromacs.org/pipermail/gmx-users/2009-October/045569.htmlconcerned
>> > on the develop of a new force field.
>> > It seems that If I wanna use a force field haven't been
>> > incooperate into the gromacs' extant version, What I need to do only is
>> > to make some new files with suffixes like .rtp / .hdb / nb.itp / bon.itp
>> > to contain the new force field parameters.
>> > This may certainly work out
>> > for pdb2gmx programme, But will it also work out for another programmes
>> > like mdrun?
>> Well, it will, because pdb2gmx builds topologies that grompp can parse
>> into input for mdrun.
>> > Cause maybe the forcefield potential function are different
>> > from any other forcefileds contained in the gromacs. Then what others
>> > can I do to finally introduce a totally new force field to gromacs?
>> Have a look at all the possibilities GROMACS already knows about in
>> chapter 4, and consider also the use of table-lookups for two-body
>> functions (manual 6.7.2). IIRC many-bodied functions won't work yet.
>> Hey Mark,
>> Thanks very much for your benevolence. Another question, How can I
>> set up a new functions? Where should they be located? What do you mean when
>> you talk about "table-lookups for two-body functions"? Where should the
>> lookups take place?
>> When I use "man mdrun" to find a "-table" option for table-lookup,
>> it obviously indicates an input file **.xvg, What can **.xvg file do? How
>> should it be created? What is the content in it?
>> Thank a lot and thanks in advance!
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