<div>Thanks M!</div>
<div> </div>
<div>I am using the standard 6-12 tables available with the gromacs package. For -table and -tablep options to start with.</div>
<div> </div>
<div>I want to understand 1 thing. The forcefield files and the topology file specifies sigma and epsilon parameters. If I change the combination rule to 1 in the forcefield.itp file, and use tables, how does gromacs convert the sigma, epsilon values in the topology file to C6 and C12?</div>
<div> </div>
<div>Pooja<br><br></div>
<div class="gmail_quote">On Fri, Sep 24, 2010 at 7:07 PM, ms <span dir="ltr"><<a href="mailto:devicerandom@gmail.com">devicerandom@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi,<br><br>Clarification: I may not be able to help you directly but I can suggest you which information you should perhaps give us to enable people more knowledgeable than me to help.
<div class="im"><br><br>On 24/09/10 17:33, Sai Pooja wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">I use combination rule 1; but I also define all tabulated interactions for<br>all possible *pairs* under the [ nonbond_params ] section, so the<br>
combination rule actually doesn't matter much.<br></blockquote><br><br>Are you suggesting that I can change the combination rule in the<br>forcefield.itp file but I must also supply a table for pairs using -tablep<br>
option for this to work?<br></blockquote><br></div>I am not "suggesting": I am only saying what I am doing :)
<div class="im"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Does this mean that one cannot use tables with forcefield parameters?<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br></blockquote><br></blockquote><br>Clarification: I want to use forcefield parameters with user defined tables<br>
i.e. I want to use sigma and epsilon values generated by pdb2gmx along<br>with a user-defined modified potential energy function using tables.<br></blockquote><br></div>This is absolutely doable -I do it everyday, in fact. So, don't despair. :)<br>
<br>Now, it seems that you talked about a problem with convergence of the SETTLE algorithm. I know little about it, but, couldn't it simply be that your tables are "wrong" (that is, they don't play well with algorithms?) What is their shape, actually, and on which atomtypes/groups are you applying your table? What is the forcefield you are using along with the table?<br>
<font color="#888888"><br>M.</font>
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