Hello again <div><br></div><div>I have tried to do as you suggest and use tables but I have a new problem. First let me describe my process and then you can let me know if there is anything wrong in the stages:</div><div>
<br></div><div>OK so first you include the following directives into the mdp file:</div><div><br></div><div>coulombtype = pme (or whatever sort of coulomb interaction you are using)</div><div>vdw-type = user<br><br></div>
<div><div>energygrps = Ca CCA OCA OW HW</div><div>energygrp_table = Ca OCA Ca CCA OCA OCA OCA OW OCA HW</div><div><br></div><div>Gromacs is then (at some stage) going to look for a series of files called</div><div>
<br></div><div>table.xvg - which is the default 6-12 Lennard Jones that will be used for most of the atoms</div><div>table_Ca_OCA.xvg - which are the Buckingham interactions between your various atom types. </div><div>
table_Ca_CCA.xvg</div><div>table_OCA_OCA.xvg</div><div>table_OCA_OW.xvg</div><div>table_OCA_HW.xvg</div><div><br></div><div>These files have the format (and contents) described in section 6.7 of the manual. Finally, you define the various energy groups Ca, OCA and so on in your index.ndx file.</div>
<div><br></div><div>The problem is that grompp gives me the following error:</div><div><br></div><div>"atoms 1 and 2 in charge group 1 of molecule type 'SOL' are in different energy groups"</div><div><br>
</div><div>(incidentally these atoms 1 and 2 are OW and HW)</div><div><br></div><div>Does this mean that I cannot use different tabulated potentials for different atoms in a molecules? By which I mean that I can't use different tabulated potentials for the OW Ca and HW Ca interactions for example?</div>
<div><br></div><div>Final question, as its not clear to me from the manual, if you use a tabulated potential for Lennard Jones and you use mix type 2 (so are you are providing epsilon and sigma in the input rather than A and B) does gromacs still know that it has to manipulate the input parameters in order to get the coefficients of the (tabulated) g(r) and h(r) dispersion and repulsion functions (I mean the g(r) and h(r) defined in section 6.7 of the manual here)? At the same time does it also know not to do anything to the parameters you input for the (tabulated) buckingham potentials (as for a buckingham you are providing A and C)?</div>
<div><br></div><div>Many thanks in advance</div><div>Gareth</div><div><br></div><div><br></div><div><br></div></div><div><div class="gmail_quote">On Wed, Mar 24, 2010 at 2:25 AM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br>
<br>
----- Original Message -----<br>
From: Matthew Watkins <<a href="mailto:matthew.watkins@ucl.ac.uk">matthew.watkins@ucl.ac.uk</a>><br>
Date: Wednesday, March 24, 2010 2:59<br>
Subject: Re: [gmx-users] Using lennard jones and buckingham terms simultaneously<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
<br>
> Hi Gareth,<br>
><br>
> as Vitaly suggested tabulated potentials seem to be the only way<br>
> to go, it took me a while to get up to speed on the Gromacs way<br>
> of doing this, so get in touch if you wish.<br>
><br>
> The tables for buck potentials need to include the standard 1/r6<br>
> term whilst what would be the 1/r12 term needs to contain exp(-<br>
> Bx.rho), the C6 and C12 coefficients can then be put in a<br>
> standard nonbonded section. You'll need a separated table<br>
> for each pair of interactions that interact with buckingham<br>
> potential. Each pair must be an energy group as well.<br>
><br>
> If there is a simpler method I'd love to hear it.<br>
<br>
</div>There's probably not a simpler method because it's not a widely-used procedure. It shouldn't be used at all unless you have established that the combination of functional forms is effective...<br>
<font color="#888888"><br>
Mark<br>
</font><div><div></div><div class="h5">--<br>
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