please stop mailing me, i am tired of all this mails<BR><BR><B><I>"Mu Yuguang (Dr)" <YGMu@ntu.edu.sg></I></B> wrote: <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid"> <META content="Microsoft Word 11 (filtered medium)" name=Generator> <STYLE> v\:* {behavior:url(#default#VML);} o\:* {behavior:url(#default#VML);} w\:* {behavior:url(#default#VML);} .shape {behavior:url(#default#VML);} </STYLE> <?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:SmartTagType name="Street" namespaceuri="urn:schemas-microsoft-com:office:smarttags"></o:SmartTagType><o:SmartTagType name="PlaceName" namespaceuri="urn:schemas-microsoft-com:office:smarttags"></o:SmartTagType><o:SmartTagType name="PlaceType" namespaceuri="urn:schemas-microsoft-com:office:smarttags"></o:SmartTagType><o:SmartTagType name="place" namespaceuri="urn:schemas-microsoft-com:office:smarttags"></o:SmartTagType><o:SmartTagType
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class=MsoNormal><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial">Dear Huey Ling,<o:p></o:p></SPAN></FONT></div> <div class=MsoNormal><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial">In principle it is applicable. Then such REMD can be termed as Hamiltonian REMD instead of canonical temperature REMD.<o:p></o:p></SPAN></FONT></div> <div class=MsoNormal><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial"><o:p> </o:p></SPAN></FONT></div> <DIV> <div class=MsoNormal><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial">Dr. Yuguang Mu</SPAN></FONT><FONT color=navy><SPAN style="COLOR: navy"><o:p></o:p></SPAN></FONT></div> <div class=MsoNormal><?xml:namespace prefix = st1 ns = "urn:schemas-microsoft-com:office:smarttags" /><st1:place w:st="on"><st1:PlaceType w:st="on"><FONT face=Arial
color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial">School</SPAN></FONT></st1:PlaceType><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial"> of <st1:PlaceName w:st="on">Biological</st1:PlaceName></SPAN></FONT></st1:place><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial"> Sciences</SPAN></FONT><FONT color=navy><SPAN style="COLOR: navy"><o:p></o:p></SPAN></FONT></div> <div class=MsoNormal><st1:Street w:st="on"><st1:address w:st="on"><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial">60 Nanyang Drive</SPAN></FONT></st1:address></st1:Street><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial"> </SPAN></FONT><FONT color=navy><SPAN style="COLOR: navy"><o:p></o:p></SPAN></FONT></div> <div class=MsoNormal><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE:
10pt; COLOR: navy; FONT-FAMILY: Arial">Nanyang Technological Uiversity</SPAN></FONT><FONT color=navy><SPAN style="COLOR: navy"><o:p></o:p></SPAN></FONT></div> <div class=MsoNormal><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial">Singapre</SPAN></FONT><FONT color=navy><SPAN style="COLOR: navy"><o:p></o:p></SPAN></FONT></div> <div class=MsoNormal><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial">Tel: +65-63162885</SPAN></FONT><FONT color=navy><SPAN style="COLOR: navy"><o:p></o:p></SPAN></FONT></div> <div class=MsoNormal><FONT face=Arial color=navy size=2><SPAN style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial">email:ygmuATntu.edu.sg</SPAN></FONT><o:p></o:p></div></DIV> <DIV> <DIV class=MsoNormal style="TEXT-ALIGN: center" align=center><FONT face="Times New Roman" size=3><SPAN style="FONT-SIZE: 12pt"> <HR tabIndex=-1 align=center width="100%" SIZE=2>
</SPAN></FONT></DIV> <div class=MsoNormal><B><FONT face=Tahoma size=2><SPAN style="FONT-WEIGHT: bold; FONT-SIZE: 10pt; FONT-FAMILY: Tahoma">From:</SPAN></FONT></B><FONT face=Tahoma size=2><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Tahoma"> gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <B><SPAN style="FONT-WEIGHT: bold">On Behalf Of </SPAN></B>Huey Ling Tan<BR><B><SPAN style="FONT-WEIGHT: bold">Sent:</SPAN></B> Tuesday, November 13, 2007 2:24 AM<BR><B><SPAN style="FONT-WEIGHT: bold">To:</SPAN></B> Discussion list for GROMACS users<BR><B><SPAN style="FONT-WEIGHT: bold">Subject:</SPAN></B> [gmx-users] REMD As A Function of Distance Between 2 Chains</SPAN></FONT><o:p></o:p></div></DIV> <div class=MsoNormal><FONT face="Times New Roman" size=3><SPAN style="FONT-SIZE: 12pt"><o:p> </o:p></SPAN></FONT></div> <div class=MsoNormal><SPAN class=q><FONT face="Times New Roman" size=3><SPAN style="FONT-SIZE: 12pt">Hi all,</SPAN></FONT></SPAN><BR><BR><SPAN
class=q>Is it feasible to do parallel tempering (replica exchange) as a function of distance with umbrella sampling applied?</SPAN><BR><BR><SPAN class=q>I can do REMD for a system containing 2 peptide chains as a function as temperatures, where I grompp each of the systems at different temperatures, and then gather the fullmd.tpr files in one folder with the script I want for full md run. </SPAN><BR><BR><SPAN class=q>But what if I want to do REMD as a function of distances (for example at 0.4, 0.6, 0.8, 1.0 nm between the chains, defined in the pull.ppa file), at a fixed temperature, with umbrella sampling applied? If this can be done, how should I write the script for the full md run so that each of the pull.ppa files can recognise the system that it suppose to pull? </SPAN><BR><BR><SPAN class=q>If anyone know how this can be done?</SPAN><BR><BR><SPAN class=q>Many thanks.</SPAN><BR clear=all><BR>-- <BR>Best regards,<BR>Huey Ling
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