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<DIV><BR>In the name of God</DIV>
<DIV>Hello dear Tsjerk A. Wassenaar </DIV>
<DIV>Tanke you very much for your guide. I want to do only energy
minimization and not MD after it.Must I use ffG43b1 and emtol for cg
lesser of emtol for steep .? When do we must use ffG43b1.?<BR>Thank you very
much in advance<BR>Institute of Biochemistry and
Biophysics (IBB)<BR>Tehran University <BR>P.O.box 1417614411<BR>Tehran
<BR>Iran <BR><BR><BR></DIV>
<BLOCKQUOTE style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px;
BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">-----Original
Message-----<BR>From: "Tsjerk Wassenaar" <tsjerkw@gmail.com><BR>To:
"Discussion list for GROMACS users" <gmx-users@gromacs.org><BR>Date:
Thu, 23 Feb 2006 11:02:25 +0100<BR>Subject: Re: [gmx-users] Minimization in
vacuo<BR><BR><BR>Hi Institute of Biochemistry and Biophysics (or can I say
IBB? :) ),<BR><BR>
<DIV><SPAN class=gmail_quote>On 2/23/06, <B class=gmail_sendername>Mahnam</B>
<<A
href="/WorldClient.dll?Session=IRGXIMI&View=Compose&To=mahnam@ibb.ut.ac.ir&New=Yes">
mahnam@ibb.ut.ac.ir </A>> wrote:</SPAN>
<BLOCKQUOTE class=gmail_quote style="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt
0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid">
<DIV><BR>In the name of God</DIV>
<DIV>Hello gmx users :</DIV>
<DIV>I want to do energy minimization in vacuo .Must I select ffG43b1 and
emtol for cg lesser of emtol for steep similar to " <FONT
face=TimesNewRoman,Bold size=5><FONT size=2>GROMACS Tutorial for Drug ?
Enzyme Complex ".?</FONT></FONT></DIV></BLOCKQUOTE>
<DIV><BR>If you're going to do a simulation afterwards in solution, don't
bother. ffG43b1 is for running simulations in vacuum, energy minimization is
just to get rid of these bad contacts in the structure. <BR></DIV><BR>
<BLOCKQUOTE class=gmail_quote style="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt
0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid">
<DIV>Thank you very much in advance<BR>Institute of Biochemistry
and Biophysics (IBB)<BR>Tehran University <BR>P.O.box
1417614411<BR>Tehran <BR>Iran <BR></DIV></BLOCKQUOTE></DIV><BR>And talking
about nettiquette.., please sign your posts. That way, we know just that bit
more about who we're dealing with and how to address you.<BR><BR>Cheers,<BR>
<BR>Tsjerk<BR clear=all><BR>-- <BR><BR>Tsjerk A. Wassenaar, M.Sc.<BR>
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<BR>Dept.
of Biophysical Chemistry<BR>University of Groningen<BR>Nijenborgh 4 <BR>
9747AG Groningen, The Netherlands<BR>+31 50 363 4336<BR></BLOCKQUOTE>
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