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Lloyd thank you very much for your answer!<BR>
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I'm going to check it out...<BR>
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Best regards,<BR>
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Gal <BR>
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> Date: Mon, 12 Sep 2011 10:34:59 +0200<BR>> From: lloyd.riggs@gmx.ch<BR>> To: gmx-users@gromacs.org<BR>> Subject: [gmx-users] RE:g_lie<BR>> <BR>> Message: 1<BR>> Date: Sun, 11 Sep 2011 13:01:28 +0200<BR>> From: <gal.fradin@live.biu.ac.il><BR>> Subject: [gmx-users] g_lie<BR>> To: <gmx-users@gromacs.org><BR>> Message-ID: <BLU160-W601D2AB913084C46676AFEE9030@phx.gbl><BR>> Content-Type: text/plain; charset="windows-1255"<BR>> <BR>> <BR>> Greetings to all!<BR>> <BR>> I have a question for the g_lie function users...<BR>> <BR>> Is there anyone who used this function successfully including the -Elj and -Eqq options???<BR>> <BR>> When I'm trying to use this function with the above mentioned options I'm getting Zeros for both Elj and Eqq<BR>> <BR>> or any other value which I set using the command... for instance if I set the Elj to be 1 then the results are 'ones'...<BR>> <BR>> It seems like a bug... <BR>> <BR>> I'm using the 4.5.3 version...<BR>> <BR>> <BR>> thanks in advance,<BR>> <BR>> Gal <BR>> <BR>> I have. It crankes out good values for small molecules <30 atoms, but is way off for large molecules (ie proteins of 100 amino acids or more). It suggest in the paper and gromacs slidshow that the alpha and beta, or perhaps a gamma function need to be determined for 100+ protein protein interactions, such as was done to achieve the averidged values used for the small molecules, to be determine properly for the electrostatic and coulombic contributions. <BR>> <BR>> You have to determine the Elj or Eqq first using g_energy, or another analysis. From what I can tell, it uses the averidges over a run for state B or A and then just does the Math function described in the paper or gromacs manual.<BR>> -- <BR>> NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie! <BR>> Jetzt informieren: http://www.gmx.net/de/go/freephone<BR>> -- <BR>> gmx-users mailing list gmx-users@gromacs.org<BR>> http://lists.gromacs.org/mailman/listinfo/gmx-users<BR>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<BR>> Please don't post (un)subscribe requests to the list. Use the <BR>> www interface or send it to gmx-users-request@gromacs.org.<BR>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<BR></DIV>                                            </div></body>
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