Oh almost forgot you also have to put<div><br></div><div>vdw-type = user</div><div><br></div><div>in the mdp file. As this tell gromacs to read in the tables.</div><div><br></div><div>Gareth <br><br><div class="gmail_quote">
On Thu, Apr 1, 2010 at 3:25 PM, Gareth Tribello <span dir="ltr"><<a href="mailto:gareth.tribello@gmail.com">gareth.tribello@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi<div><br></div><div>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:</div>
<div><br></div><div>V(r) = (q_i q_j / 4 pi eps_0 ) f(r) + A g(r) + C h(r)</div><div><br></div><div>Your table should have seven columns which are:</div><div><br></div><div>r, f(r) , f'(r) , g(r), g'(r) , h(r), h'(r)</div>
<div><br></div><div>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.</div>
<div><br></div><div>As an example if you were using Lennard Jones with a coulomb interaction</div><div><br></div><div>f(r) = 1/r</div><div>g(r) = -1/r**6</div><div>h(r) = 1/r**12</div><div><br></div><div>You then need to put the tables you are using in the directory in which you are running gromacs.</div>
<div><br></div><div>Ciao</div><div>Gareth</div><div><font color="#888888"> <br><br></font><div class="gmail_quote"><div><div></div><div class="h5">On Thu, Apr 1, 2010 at 12:08 PM, DreamCatcher <span dir="ltr"><<a href="mailto:huangshuping1987@gmail.com" target="_blank">huangshuping1987@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div></div><div class="h5">Message: 5<br>
Date: Thu, 01 Apr 2010 16:30:44 +1100<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] custom forcefields or a new forcefields<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4BB42F84.9050703@anu.edu.au" target="_blank">4BB42F84.9050703@anu.edu.au</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<div><br>
On 01/04/10 16:20, DreamCatcher wrote:<br>
> Hello gmx-users,<br>
> I have just look through the mail-list to find this<br>
> <a href="http://lists.gromacs.org/pipermail/gmx-users/2009-October/045569.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2009-October/045569.html</a> concerned<br>
> on the develop of a new force field.<br>
> It seems that If I wanna use a force field haven't been<br>
> incooperate into the gromacs' extant version, What I need to do only is<br>
> to make some new files with suffixes like .rtp / .hdb / nb.itp / bon.itp<br>
> to contain the new force field parameters.<br>
Yes.<br>
> This may certainly work out<br>
> for pdb2gmx programme, But will it also work out for another programmes<br>
> like mdrun?<br>
Well, it will, because pdb2gmx builds topologies that grompp can parse<br>
into input for mdrun.<br>
> Cause maybe the forcefield potential function are different<br>
> from any other forcefileds contained in the gromacs. Then what others<br>
> can I do to finally introduce a totally new force field to gromacs?<br>
Have a look at all the possibilities GROMACS already knows about in<br>
chapter 4, and consider also the use of table-lookups for two-body<br>
functions (manual 6.7.2). IIRC many-bodied functions won't work yet.<br><br>
Mark<br></div>
------------------------------
<br><br>Hey Mark,<br> 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? <br>
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?<br>
Thank a lot and thanks in advance!<br>
celeste<br> 2010-4-1<br>
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