<DIV>Thank you very much for your replay.</DIV>
<DIV>I agree with you that it is better if you work with the complete sistem, unfortunatly the sistem is very hugh, for that rason I tried to reduce my sistem cutting the protein (bad idea I think).</DIV>
<DIV>Could you give another alternative. It could be a good idea if I use freeze atoms????? If I do that, Will I need a non equilibrium dinamic????.</DIV>
<DIV>the value of G that I refer is the result after the use of g_lie, next to the resul appear a number like this (xxxxx), what does it mean?, sometimes appear a word (nan).</DIV>
<DIV> </DIV>
<DIV>I used beta 0.01 and lamda 0.15</DIV>
<DIV> </DIV>
<DIV>Thak you very much</DIV>
<DIV>Cesar<BR><BR><B><I>Anton Feenstra <feenstra@few.vu.nl></I></B> wrote:</DIV>
<BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">Cesar Lopez wrote:<BR><BR>> Dear users gromacs<BR>> <BR>> I am running a molecular simuation using a sistem between RNA polymerase and Ryfampicin, well I have cut the polymerase using only the active site where the ryfampicin dock, and then I have used the LIE mthod to calculate the free gibs energy.<BR>> <BR>> My question are:<BR>> <BR>> Why appear a simbol (nan) nera to the result of G<BR>> What does it mean?<BR>> sometimes appear numbers ( 22.222 for example), but when you modify the beta and alfa parameters it seems that it reduce the number.<BR><BR>You should be aware that some versions of Gromacs (notably, 3.1, I'm not <BR>sure of 3.2) have a bug in g_lie. You can use g_energy and a pocket <BR>calculator to do the calculations yourself, however.<BR><BR>I'm not sure it is sensible to use g_lie on a 'cutout' portion of you <BR>system, normally on
e would
want the interaction energy between ligand <BR>(Ryfampicin, in this case I assume) and the rest of the system <BR>(RNApolymerase *and* solvent), and compare those with the interaction <BR>energy between ligand and solvent only (from a separate simulation of <BR>ligand in solvent!).<BR><BR>- Which 'results of G' are your referring to?<BR>- modifying beta and alpha changes your free energy estimate, obviously. <BR>Which values have you used? Which changes did you see?<BR><BR><BR>-- <BR>Groetjes,<BR><BR>Anton<BR><BR>* NOTE: New Phone & Fax numbers (below) *<BR><BR>_____________ _______________________________________________________<BR>| | |<BR>| _ _ ___,| K. Anton Feenstra |<BR>| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |<BR>|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |<BR>| \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610 |<BR>| | Feenstra@few.vu.nl - www.few.vu.nl/~feenstra/ |<BR>| | "If You See Me Getting High, Kno
ck Me
Down" (RHCP) |<BR>|_____________|_______________________________________________________|<BR><BR>_______________________________________________<BR>gmx-users mailing list<BR>gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<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></BLOCKQUOTE><p>
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