Hi 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. Ciao Gareth On Thu, Apr 1, 2010 at 12:08 PM, DreamCatcher <[email protected]>wrote: > Message: 5 > Date: Thu, 01 Apr 2010 16:30:44 +1100 > From: Mark Abraham <[email protected]> > Subject: Re: [gmx-users] custom forcefields or a new forcefields > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > 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. > Yes. > > 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. > > Mark > ------------------------------ > > 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! > > celeste > > 2010-4-1 > > -- > gmx-users mailing list [email protected] > http://lists.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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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