Thanks Mark :). <br><br><div class="gmail_quote">On Tue, Sep 7, 2010 at 10:06 PM, 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: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div><div></div><div class="h5"><br><br>----- Original Message -----<br>From: Sai Pooja <<a href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a>><br>Date: Sunday, September 5, 2010 8:19<br>Subject: [gmx-users] Tables and forcefield parameters<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Hi,<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>ques1:<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I have 3 energy groups.<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I am interested in using tables for LJ and coulomb interactions for Group1-group2 interactions. <br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>For all other interactions:<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>1) Group1-group1 -all interactions-bonded and non-bonded<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> 2) Group2-group2 -all interactions -bonded and non-bonded<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>3) All possible combinations for group3<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I want to use gromacs defined standard energy functions.<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>For all other types of interactions, e.g. 1-4 pair interactions and bonded interactions I would like to use gromacs defined interactions. <br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>And for all these cases, I am still looking to use parameters defined by the forcefield. I would like to specify that I am will be using a functional form in the tables differing from coulomb and 6-12 LJ interactions by a numeric constant.<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Is it possible? If not entirely, which is possible? Any suggestions on which part might be easier to program?<br>
<br></div></div>You just take the normal table and multiply the values in it by the constant. Then use that table for the energygrp_table entry for the appropriate groups. No coding required. Manual 6.7.2 points you at some starting points for tables to modify.<br>
<font color="#888888"><br>Mark
</font><br>--<br>
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