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Hi,<BR>
I am trying to simulate an organic system which has a planar-square Pt center. I am following the methodology employed in JACS 2008, 10040 (where they use amber calculations). There, they use 2 dummy atoms to mantain the planar square geometry of the metal. <BR>
I have built my system with no dummy atoms, using GAFF and converted it into Gromacs, so now I have a .gro and a .top file.<BR>
I have introduced then the dummy atoms, in the .gro and in the topology file, but I get errors complaining about these extra atoms has mass 0. <BR>
I have read the manual and also looked at the GMX list, and I have found that other people have also found problems of these type. I have read that in case such as acetonitrile the advice was to <SPAN style="mso-ansi-language: EN-GB" lang=EN-GB>redistribute the mass over N and CH3 such that centre of mass is </SPAN><SPAN style="mso-ansi-language: EN-GB" lang=EN-GB>unchanged and inertia tensor is not modified too much either.</SPAN><BR>
<SPAN style="mso-ansi-language: EN-GB" lang=EN-GB>Should I do something similar in my case? Which mass should I redistribute? The mass of the whole molecule? </SPAN><BR>
<SPAN style="mso-ansi-language: EN-GB" lang=EN-GB></SPAN> <BR>
<SPAN style="mso-ansi-language: EN-GB" lang=EN-GB>Thank you very much for your help.</SPAN><BR>
<SPAN style="mso-ansi-language: EN-GB" lang=EN-GB></SPAN> <BR>
<SPAN style="mso-ansi-language: EN-GB" lang=EN-GB>Best wishes,</SPAN><BR>
<SPAN style="mso-ansi-language: EN-GB" lang=EN-GB></SPAN> <BR>
<SPAN style="mso-ansi-language: EN-GB" lang=EN-GB>Dr. Rebeca Garcia</SPAN><BR>
<SPAN style="mso-ansi-language: EN-GB" lang=EN-GB>Universidad de A Coruña</SPAN><BR>
<SPAN style="mso-ansi-language: EN-GB" lang=EN-GB>Spain</SPAN><BR> <br /><hr />Comparte tus fotos con tus amigos. Más fácil con <a href='http://download.live.com' target='_new'>Windows Live</a></body>
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