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<DIV><FONT face=Arial size=2><FONT face="Times New Roman" size=3><FONT
face=Arial size=2>Thanks, for your fast reply and for the
code.</FONT></FONT></FONT></DIV>
<DIV><FONT face=Arial size=2>I had a look in the code but I can't find the
swapping probability for hamiltonian replica exchange. I expected this in
repl_ex.c but I can't find anything like it. I could not locate another
function in md.c or mdrun.c to do the hamiltonion replica exchange. Could you
help me al little further here were to look?</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
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<DIV><FONT face=Arial size=2>thanks! </FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>servaas</FONT></DIV>
<DIV><FONT face=Arial size=2><FONT face="Times New Roman" size=3><FONT
face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT><BR>Date: Fri, 15 Feb 2008 11:56:16
+0100<BR></FONT><FONT face="Times New Roman" size=3><BR>Hi,<BR><BR>My own server
is unfortunately down since it was hacked last week and <BR>we were anyway
about to move from Joomla to Dekiwiki, but I've <BR>uploaded a copy to the
ftp site. Have a look in<BR><BR></FONT><A
href="ftp://ftp.gromacs.org/pub/tmp/multilambda/"><FONT face="Times New Roman"
size=3>ftp://ftp.gromacs.org/pub/tmp/multilambda/</FONT></A><BR><BR><FONT
face="Times New Roman" size=3>Not sure if it's useful for your stuff, and since
I haven't gotten <BR>much feedback for it yet you shouldn't use it for
production purposes <BR>without significant testing. You've been warned,
have fun ;-)<BR><BR>Cheers,<BR><BR>ERik<BR><BR>Have a look at the<BR>On Feb 15,
2008, at 11:22 AM, servaas michielssens wrote:<BR><BR>> Hi,<BR>><BR>> I
am planning to do a hamiltonian replica exchange simulation and I <BR>>
came acros this message. I am wondering what the status of this work
<BR>> is and if it is possible to obtain a copy of the code to do
<BR>> hamiltonain replica exchange. Or if not some suggestion on the
best <BR>> way to implement the extra energy evalution with a topoly
on <BR>> anonther node.<BR>><BR>><BR>> kind
regards,<BR>><BR>> servaas<BR>><BR>><BR>> Hi
David,<BR>><BR>> On Nov 2, 2007, at 5:19 PM, David Mobley wrote:<BR>>
><BR>> >> There is nearly no difference between the two as far as
the replica<BR>> >> stuff is concerned.<BR>> >> It will be
more work to (correctly) extract the foreign lambda <BR>>
energy<BR>> >> than it is to modify<BR>> >> the actual
exchange criterion. Erik did some work on foreign lambda<BR>> >>
calculations,<BR>> >> but I don't know what the status of that
is.<BR>> >><BR>> >> I guess the head branch would be the
better option, especially if <BR>> you<BR>> >> want to
run<BR>> >> each replica over multiple cpu's.<BR>> ><BR>> >
Maybe Erik can weigh in on whether this is "for sure", but my<BR>> >
understanding is that he's almost done with the "foreign lambda"<BR>> >
implementation (he indicated having a testable version over this<BR>> >
coming weekend).<BR>><BR>> Yes, I'll start to send this to David &
John for testing, but in a<BR>> week or so we should have code for other
people to play with too.<BR>><BR>> Cheers,<BR>><BR>>
Erik</FONT><BR></DIV></FONT></BODY></HTML>