Lloyd thank you very much for your answer! I'm going to check it out... Best regards, Gal
> Date: Mon, 12 Sep 2011 10:34:59 +0200 > From: [email protected] > To: [email protected] > Subject: [gmx-users] RE:g_lie > > Message: 1 > Date: Sun, 11 Sep 2011 13:01:28 +0200 > From: <[email protected]> > Subject: [gmx-users] g_lie > To: <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="windows-1255" > > > Greetings to all! > > I have a question for the g_lie function users... > > Is there anyone who used this function successfully including the -Elj and > -Eqq options??? > > When I'm trying to use this function with the above mentioned options I'm > getting Zeros for both Elj and Eqq > > 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'... > > It seems like a bug... > > I'm using the 4.5.3 version... > > > thanks in advance, > > Gal > > 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. > > 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. > -- > NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie! > Jetzt informieren: http://www.gmx.net/de/go/freephone > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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