[gmx-users] RE:g_lie

gal.fradin at live.biu.ac.il gal.fradin at live.biu.ac.il
Mon Sep 12 11:17:38 CEST 2011

Lloyd thank you very much for your answer!
I'm going to check it out...
Best regards,

> Date: Mon, 12 Sep 2011 10:34:59 +0200
> From: lloyd.riggs at gmx.ch
> To: gmx-users at gromacs.org
> Subject: [gmx-users] RE:g_lie
> Message: 1
> Date: Sun, 11 Sep 2011 13:01:28 +0200
> From: <gal.fradin at live.biu.ac.il>
> Subject: [gmx-users] g_lie
> To: <gmx-users at gromacs.org>
> Message-ID: <BLU160-W601D2AB913084C46676AFEE9030 at phx.gbl>
> 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.
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