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<DIV><FONT face=Arial size=2>Thank you very much, David, for your
quick response and comment, and thanks Dallas for your suggestion to use
"VMD" and "trjconv" to center the protein back into the water box. I would like
to try that very soon.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I have one more question that from output (.edr,
.trr) of a ligand-protein complex MD study, may i calculate the binding free
energy of small ligand???? If possible, what's the command,
please???</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Thanks,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>nancy</FONT></DIV>
<DIV> </DIV>
<BLOCKQUOTE
style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=dallas.warren@vcp.monash.edu.au
href="mailto:dallas.warren@vcp.monash.edu.au">Dallas Warren</A> </DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">Discussion list for GROMACS users</A>
</DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Wednesday, March 23, 2005 2:16
PM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> Re: [gmx-users] protein
wandering away</DIV>
<DIV><BR></DIV>
<BLOCKQUOTE class=cite cite="" type="cite">I just simulated a 5ns MD by
GROMACS FF for a small system containing 160<BR>amino acid residues in a
water box. The thing confused me was that the<BR>protein started to close
one edge of the water box around 2ns and part of it<BR>movedout of the box
later. At the end of the 5ns calculation, most of<BR>protein was out of the
box, while water molecules were still in the box.</BLOCKQUOTE><BR>That is just
the PBC acting. The water molecules are so small that, pretty much as
soon as they wander out of the box visually, they then reappear on the
opposite side. However, with something as large as a protein, as it
moves out the side of the box, to visually keep it within the rest of the
water, you would have to break the molecule. And that isn't done, so it
seems that the protein is sticking out into a "vacuum". But if you check
the opposite side of the box, there will be a hole in the water where the
protein molecule is inserted. Using VMD you can easily turn on the boxes
in each periodic direction, so that you can easily see that
happening.<BR><BR>Just used trjconv to center the protein back in the
simulation box if you want to.<BR><BR>Catch ya,<BR><X-SIGSEP>
<P></X-SIGSEP><B>Dr. Dallas Warren<BR></B><I>Lecturer<BR></I>Department of
Pharmaceutical Biology and Pharmacology<BR>Victorian College of Pharmacy,
Monash University<BR>381 Royal Parade, Parkville VIC 3010<BR><FONT
color=#0000ff><U>dallas.warren@vcp.monash.edu.au<BR></U></FONT>+61 3 9903
9574<BR><FONT
face="Times New Roman, Times">--------------------------------------------------------------------------<BR><I>When
the only tool you own is a hammer, every problem begins to resemble a
nail.</FONT></I>
<P>
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