<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META content="text/html; charset=gb2312" http-equiv=Content-Type>
<META name=GENERATOR content="MSHTML 8.00.6001.18702">
<STYLE>@font-face {
        font-family: ;
}
@font-face {
        font-family: Verdana;
}
@font-face {
        font-family: @;
}
@page Section1 {size: 595.3pt 841.9pt; margin: 72.0pt 90.0pt 72.0pt 90.0pt; layout-grid: 15.6pt; }
P.MsoNormal {
        TEXT-JUSTIFY: inter-ideograph; TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt; FONT-FAMILY: "Times New Roman"; FONT-SIZE: 10.5pt
}
LI.MsoNormal {
        TEXT-JUSTIFY: inter-ideograph; TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt; FONT-FAMILY: "Times New Roman"; FONT-SIZE: 10.5pt
}
DIV.MsoNormal {
        TEXT-JUSTIFY: inter-ideograph; TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt; FONT-FAMILY: "Times New Roman"; FONT-SIZE: 10.5pt
}
A:link {
        COLOR: blue; TEXT-DECORATION: underline
}
SPAN.MsoHyperlink {
        COLOR: blue; TEXT-DECORATION: underline
}
A:visited {
        COLOR: purple; TEXT-DECORATION: underline
}
SPAN.MsoHyperlinkFollowed {
        COLOR: purple; TEXT-DECORATION: underline
}
SPAN.EmailStyle17 {
        FONT-STYLE: normal; FONT-FAMILY: Verdana; COLOR: windowtext; FONT-WEIGHT: normal; TEXT-DECORATION: none; mso-style-type: personal-compose
}
DIV.Section1 {
        page: Section1
}
UNKNOWN {
        FONT-SIZE: 10pt
}
BLOCKQUOTE {
        MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px; MARGIN-LEFT: 2em
}
OL {
        MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px
}
UL {
        MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px
}
</STYLE>
</HEAD>
<BODY style="MARGIN: 10px; FONT-FAMILY: verdana; FONT-SIZE: 10pt">
<DIV><FONT color=#000080 size=2 face=Verdana>
<DIV>Hi&nbsp;all:</DIV>
<DIV>&nbsp;</DIV>
<DIV>It&nbsp;is&nbsp;a&nbsp;very&nbsp;good&nbsp;news&nbsp;that&nbsp;Gromacs-4.5&nbsp;is&nbsp;coming&nbsp;soon!</DIV>
<DIV>&nbsp;</DIV>
<DIV></DIV>
<DIV>I&nbsp;have&nbsp;two&nbsp;problems&nbsp;not&nbsp;very&nbsp;clearly.</DIV>
<DIV></DIV>
<DIV>First,&nbsp;Gromacs-4.5&nbsp;can&nbsp;use&nbsp;GPU&nbsp;to&nbsp;accelerate&nbsp;simulations.&nbsp;But&nbsp;in&nbsp;</DIV>
<DIV>the&nbsp;"Limitations",&nbsp;it's&nbsp;said&nbsp;that&nbsp;"Multiple&nbsp;GPU&nbsp;cards&nbsp;are&nbsp;not&nbsp;supported".</DIV>
<DIV>So&nbsp;can't&nbsp;I&nbsp;accelerate&nbsp;the&nbsp;simulations&nbsp;with&nbsp;parallel&nbsp;mdrun?&nbsp;</DIV>
<DIV>&nbsp;</DIV>
<DIV></DIV>
<DIV>Second,&nbsp;in&nbsp;Gromacs-4.5&nbsp;new&nbsp;features,&nbsp;it's&nbsp;said:</DIV>
<DIV>"Running&nbsp;on&nbsp;multi-core&nbsp;nodes&nbsp;now&nbsp;automatically&nbsp;uses&nbsp;thread-based&nbsp;parallelization".</DIV>
<DIV>If&nbsp;there're&nbsp;two&nbsp;nodes&nbsp;with&nbsp;8&nbsp;CPU&nbsp;cores&nbsp;each,&nbsp;and&nbsp;I&nbsp;use&nbsp;all&nbsp;of&nbsp;the&nbsp;CPU&nbsp;cores,&nbsp;</DIV>
<DIV>is&nbsp;there&nbsp;8&nbsp;threads&nbsp;other&nbsp;than&nbsp;8&nbsp;MPI&nbsp;processes&nbsp;in&nbsp;one&nbsp;node?&nbsp;</DIV>
<DIV>If&nbsp;true,&nbsp;do&nbsp;the&nbsp;8&nbsp;threads&nbsp;in&nbsp;one&nbsp;node&nbsp;share&nbsp;with&nbsp;one&nbsp;large&nbsp;memory?&nbsp;</DIV>
<DIV>And&nbsp;what&nbsp;is&nbsp;the&nbsp;parallelization&nbsp;scheme&nbsp;inner&nbsp;the&nbsp;node&nbsp;and&nbsp;inter&nbsp;the&nbsp;nodes?</DIV>
<DIV>&nbsp;</DIV>
<DIV></DIV>
<DIV>Appreciate&nbsp;any&nbsp;advice&nbsp;in&nbsp;advance!</DIV></FONT></DIV>
<DIV><FONT color=#000080 size=2 face=Verdana></FONT>&nbsp;</DIV>
<DIV><FONT color=#000080 size=2 face=Verdana></FONT>&nbsp;</DIV>
<DIV><FONT color=#c0c0c0 size=2 face=Verdana>2010-08-31 </FONT></DIV><FONT 
color=#000080 size=2 face=Verdana>
<HR style="WIDTH: 100px" align=left color=#b5c4df SIZE=1>
</FONT>
<DIV><FONT color=#c0c0c0 size=2 face=Verdana><SPAN>
<DIV>
<DIV><FONT size=2 face=Verdana></FONT>
<DIV>&nbsp;</DIV>
<DIV>Best </DIV>
<DIV>&nbsp;&nbsp;&nbsp; wishes</DIV>
<DIV>&nbsp;</DIV>
<DIV>Ji Xu</DIV>
<DIV></DIV>
<DIV>The&nbsp;State&nbsp;Key&nbsp;Laboratory&nbsp;of&nbsp;Multiphase&nbsp;Complex&nbsp;System</DIV>
<DIV>Institute&nbsp;of&nbsp;Process&nbsp;Engineering</DIV>
<DIV>Chinese&nbsp;Academy&nbsp;of&nbsp;Sciences</DIV>
<DIV>Beijing&nbsp;100190,&nbsp;China</DIV>
<DIV>Tel.:&nbsp;+86&nbsp;10&nbsp;8262&nbsp;3713-804&nbsp;</DIV></DIV></DIV></SPAN></FONT></DIV>
<HR color=#b5c4df SIZE=1>

<DIV><FONT size=2 face=Verdana>&nbsp;</DIV></FONT></BODY></HTML>