Oh almost forgot you also have to put vdw-type = user
in the mdp file. As this tell gromacs to read in the tables. Gareth On Thu, Apr 1, 2010 at 3:25 PM, Gareth Tribello <[email protected]>wrote: > 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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