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<DIV dir=ltr><FONT face=Arial color=#000000 size=2>Hey Javier,</FONT></DIV>
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<DIV dir=ltr><FONT face=Arial size=2>Thank you very much!</FONT></DIV>
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<DIV dir=ltr><FONT face=Arial size=2>I already read the manual, but somehow didn't get the point. Now its clear, thanks.</FONT></DIV>
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<DIV dir=ltr><FONT face=Arial size=2>Felix</FONT></DIV></DIV>
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<FONT face=Tahoma size=2><B>Von:</B> gmx-users-bounces@gromacs.org im Auftrag von Javier Cerezo<BR><B>Gesendet:</B> Mi 06.07.2011 09:40<BR><B>An:</B> gmx-users@gromacs.org<BR><B>Betreff:</B> Re: [gmx-users] Bond force constant for GROMOS<BR></FONT><BR></DIV>
<DIV>Hi Felix<BR><BR>Take a look to 4.2.1 section in the manual. Gromos force constants (k^b) has this extra nm-2 factor because they are defined as: <BR>2 k^b bij^2 = k^{b,harm} (equation 4.39 in the manual version 4.5.4)<BR><BR>So you have to divide your derived harmonic force constants (in KJ/(mol*nm^2) by 2 and bij^2 (equilibrium distance or ideal bond length as stated in gromos files) to get the gromos one (k^b). It could also be useful for you to visit the new GROMOS website as there is some free downloadable FF documentation.<BR><BR>Javier<BR><BR>El 06/07/11 08:48, Rausch, Felix escribió:
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<DIV><FONT face=Arial color=#000000 size=2>Dear Gromacs-users,</FONT></DIV>
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<DIV><FONT face=Arial size=2>I would like to add a new bond type to the ffbonded.itp of the Gromos53a6 force field. For that, I tried to obtain the force constant for my new bond by performing vibrational frequency calculations with Gaussian. With that, I obtained the force constant in mDyne/A.</FONT></DIV>
<DIV><FONT face=Arial size=2>My problem is now: How can I convert this value to kJ/(mol*nm(4)) as required for the force field? I already tried, but I only end up at kJ/(mol*nm(2)). Also arround the web I could only find a factor for conversion of mDyne/A to kJ/(mol*nm(2)). Is there any trick or hint you can give me about that?</FONT></DIV>
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<DIV><FONT face=Arial size=2>Thanks for your help,</FONT></DIV>
<DIV><FONT face=Arial size=2>Felix</FONT></DIV>
<DIV><FONT face=Arial size=2> </FONT></DIV></BLOCKQUOTE><BR><PRE class=moz-signature cols="72">--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Mua
Murcia (Spain)
Tlf.(+34)868887434</PRE></DIV></BODY></HTML>