<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><html>
<head>
<meta name="GENERATOR" content="IncrediMail 1.0">
<!--IncrdiXMLRemarkStart>
<IncrdiX-Info>
<X-FID>FLAVOR00-NONE-0000-0000-000000000000</X-FID>
<X-FVER></X-FVER>
<X-CNT>;</X-CNT>
</IncrdiX-Info>
<IncrdiXMLRemarkEnd-->
</head>
<BODY background="" bgColor=#ffffff style="BACKGROUND-POSITION: 0px 0px; SCROLLBAR-FACE-COLOR: #ebeaea; FONT-SIZE: 10pt; MARGIN: 1px; SCROLLBAR-HIGHLIGHT-COLOR: #aeaaaa; SCROLLBAR-SHADOW-COLOR: #a9a9a9; SCROLLBAR-3DLIGHT-COLOR: #e5e5e5; SCROLLBAR-ARROW-COLOR: #0846d1; FONT-FAMILY: Arial; SCROLLBAR-DARKSHADOW-COLOR: #545252" scroll="yes" ORGYPOS="0" X-FVER="2.0">
<TABLE border=0 cellPadding=0 cellSpacing=0 id=INCREDIMAINTABLE width="95%">
<TR>
<TD id=INCREDITEXTREGION width="100%" style="PADDING-RIGHT: 7px; PADDING-LEFT: 7px; FONT-SIZE: 10pt; FONT-FAMILY: Arial"
>
<DIV>Hi Justin.</DIV>
<DIV>Here we are again. We are trying to use the AFM pulling option for a
while now.</DIV>
<DIV>As you suggested a previous mail a few months ago, we installed the
updated CVS version of gromacs (20.09.2002), and we found some weird
things:</DIV>
<DIV> </DIV>
<DIV><FONT size=3><FONT size=2>1) we performed several simulations
with the following parameters:</FONT> </FONT> <BR>verbose =
yes<BR>runtype = afm<BR>group_1 = Pull-atm <BR>reference_group =
Chain-BC <BR>reftype = com<BR>direction = 0.0 0.0
1.0<BR>reverse = from_reference<BR>pullrate = 0.0000005 <BR>forceconstant
= 1500</DIV>
<DIV> </DIV>
<DIV>without constrains and a timestep = 0.0005 ps. In these
conditions, the spring position dislocated 0.01nm in 10 ps of
simulation (as expected), however the pulled_group (Pull-atm) has
translated 14 nm by this time, which is absurd. Either we are doing
something wrong, or something is not working on with the pull
code.</DIV>
<DIV> </DIV>
<DIV>2) We also tented to reproduce the same simulation in an
effective medium ( epsilon-r = 78 ) but we couldn't do it without removing
the center of mass motion, because the 'nstcom' parameter does
not accept other value than -1. Free center of mass motion is
absolutely necessary to perform the afm simulations.</DIV>
<DIV> </DIV>
<DIV>We really hope you could dedicate some time to help us. We appreciate
it a lot. Thanks in advance,</DIV>
<DIV>Alicia and Ernesto</DIV>
<DIV> </DIV>
<DIV> </DIV></TD>
</TR>
<TR>
<TD id=INCREDIFOOTER width="100%">
<TABLE cellPadding=0 cellSpacing=0 width="100%">
<TR>
<TD width="100%"></TD>
<TD align=middle id=INCREDISOUND vAlign=bottom></TD>
<TD align=middle id=INCREDIANIM vAlign=bottom></TD>
</TR>
</TABLE>
</TD>
</TR>
</TABLE><SPAN
id=IncrediStamp><SPAN dir=ltr><FONT face="Arial, Helvetica, sans-serif"
size=2>____________________________________________________<BR><FONT
face="Comic Sans MS" size=2><A
href="http://www.incredimail.com/redir.asp?ad_id=309&lang=9"><IMG alt=""
hspace=0 src="cid:FA50588C-4ACF-45D5-A110-63A479DC0392" align=baseline
border=0></A> <I>IncrediMail</I> - <B>Email has finally evolved</B> -
</FONT><A href="http://www.incredimail.com/redir.asp?ad_id=309&lang=9"><FONT
face="Times New Roman" size=3><B><U>Click
Here</U></B></FONT></A></SPAN></SPAN></FONT>
</BODY>
</html>