I understood from the gromacs manual the units for epsilon and sigma are KJ/mol and nm and the corresponding units in MOIL Kcal/mol and Angstom. But when i checked for some atoms, the epsilon values are not matching. i.e., for example i took the value of epsilon value of S from gromacs 1.8828 and divided by the conversion faction 4.184. The result is 0.45 but in MOIL the value is 0.25. I also checked some other atoms like K,Na,Cl... there also the values does not match. <br>
<br>If anybody knows where i am making mistake please teach me. Thank you.<br><br>with regards,<br>Rama<br><br><div class="gmail_quote">On Fri, Sep 17, 2010 at 2:20 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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 class="im"><br>
<br>
Ramachandran G wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi gmx-users,<br>
I would like to know the units conversion of epsilon, sigma (from non-bonded, Van der Waal interaction) from Charmm or MOIL to gromacs.<br>
Thank you.<br>
<br>
</blockquote>
<br></div>
My guess would be that each of the respective manuals would discuss whatever unit conventions are utilized. As far as Gromacs is concerned, Chapter 4 contains information about such matters, as well as Table 5.2 (and sections nearby).<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
with regards,<br>
Rama<br>
<br>
<br>
</blockquote>
<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>
<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Postdoctoral Research Scholar,<br>Department of Chemistry,<br>University of Nevada, Reno.<br>