<div>Thank you for your clarification.</div>
<div>Rama<br><br></div>
<div class="gmail_quote">On Fri, Sep 17, 2010 at 5:49 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div class="im"><br><br>Ramachandran G wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Thank you Justin,<br> You are right i am not comparing the same force field.<br> But i am still curious to know the conversion factor for epsilon from MOIL to gromacs(charmm)force field.<br>
i.e., for sulfur epsilon value of 0.25 to 1.8828. Thank you.<br><br></blockquote><br></div>If you are not comparing the same force fields, you are not likely to get the same answer. I thought I identified the fact that the value you are referring to corresponds to the MOIL implementation of OPLS-UA, which has no relationship whatsoever to the Gromacs implementation of CHARMM.<br>
<br>Dividing by 4.184 is the correct conversion factor for kcal->kJ.<br><br>-Justin<br><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">with regards,<br>Rama
<div class="im"><br><br>On Fri, Sep 17, 2010 at 5:21 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br><br><br> Ramachandran G wrote:<br><br> I understood from the gromacs manual the units for epsilon and<br> sigma are KJ/mol and nm and the corresponding units in MOIL<br> Kcal/mol and Angstom. But when i checked for some atoms, the<br>
epsilon values are not matching. i.e., for example i took the<br> value of epsilon value of S from gromacs 1.8828 and divided by<br> the conversion faction 4.184. The result is 0.45 but in MOIL the<br> value is 0.25. I also checked some other atoms like K,Na,Cl...<br>
there also the values does not match.<br><br><br> Are you comparing the same force fields? According to the MOIL<br> documentation, CHARMM is not implemented unless the user provides<br> it. However, the epsilon value of OPLS-UA sulfur (1.046), when<br>
converted to MOIL units (kcal/mol), is 0.25, which I assume is where<br> you're finding that value.<br><br> -Justin<br><br> If anybody knows where i am making mistake please teach me.<br> Thank you.<br>
<br> with regards,<br> Rama<br><br> On Fri, Sep 17, 2010 at 2:20 PM, Justin A. Lemkul<br> <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
</div>
<div class="im"> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> wrote:<br><br><br><br> Ramachandran G wrote:<br>
<br> Hi gmx-users,<br> I would like to know the units conversion of epsilon,<br> sigma<br> (from non-bonded, Van der Waal interaction) from Charmm<br> or MOIL<br> to gromacs.<br>
Thank you.<br><br><br> My guess would be that each of the respective manuals would<br> discuss<br> whatever unit conventions are utilized. As far as Gromacs is<br> concerned, Chapter 4 contains information about such matters, as<br>
well as Table 5.2 (and sections nearby).<br><br> -Justin<br><br> with regards,<br> Rama<br><br><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></div> jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> <<a href="http://vt.edu/" target="_blank">http://vt.edu</a>> <<a href="http://vt.edu/" target="_blank">http://vt.edu</a>> | (540)
<div class="im"><br> 231-9080<br><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> ========================================<br>
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<div class="h5"><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>
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