Hi<br>Gareth<br><br>Thanks for the notes on user defined potentials in GROMACS. I will go through it and will send you the feedback after I get the simulation results.<br><br><br>Thanks<br>sikandar<br><br><div class="gmail_quote">
On Sun, Apr 4, 2010 at 11:27 AM, 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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi all<div><br></div><div>I have just been stuck on this very problem of user defined potentials. When I emailed this list I was asked if I could make notes on the solution as this is a problem that seems to come up a lot. Anyway, I will send the notes to you separately Sikandar and would ask if anyone knows where should put/send them if they are to be accessible to the user community?</div>
<div><br></div><div>Many thanks</div><div>Gareth<div><div></div><div class="h5"><br><br><div class="gmail_quote">On Sun, Apr 4, 2010 at 3:47 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div><br>
<br>
Sikandar Mashayak wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi<br>
<br>
I plan to do 'fluid in channel' simulations using GROMACS 4.0.7. For that I need to use custom potential field parameters for fluid-fluid and fluid-wall interactions.<br>
<br>
So my question is that, how can I use potential table approach to specify fluid-fluid and fluid-wall interactions seperately?<br>
<br>
</blockquote>
<br></div></div>
Start with the manual, section 6.7.2, and see the table*.xvg in the /share/top subdirectory of your Gromacs installation for examples.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks<br>
sikandar<br>
<br>
</blockquote><div><div></div><div>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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