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<DIV><FONT face=Arial size=2>If you remove the pbc = xyz variable in the mdp,
the run will be *exactly* the same. Because the default value for gmx is
pbc = xyz.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Ah! And having the protein centered in the box, is
a pos-production cosmetic effect, performed by trjconv and a combination of
flags -pbc, -ur , -center. Though some MD programs do it
automatically while performing the runs.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Regards</FONT></DIV>
<DIV><FONT face=Arial size=2>Nuno</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV> </DIV>
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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=jdeng@adrik.bchs.uh.edu href="mailto:jdeng@adrik.bchs.uh.edu">Nancy
Deng</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> Tuesday, April 05, 2005 6:04
PM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> Re: [gmx-users] pbc</DIV>
<DIV><BR></DIV>
<DIV><FONT face=Arial size=2>Dear all,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I am wondering if I remove the script line: "pbc
= xyz" from my .mdp file, whether the program will automatically always center
the protein in the solvent box. Appreciate you reply, 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>
<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=fit_tone@163.com href="mailto:fit_tone@163.com">zjim</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> Monday, April 04, 2005 5:58
PM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> Re: [gmx-users] trjconv</DIV>
<DIV><BR></DIV><BR>maybe you needn't use "-n index.ndx", i always do as
"trhconv -f *.trr -s *.tpr -o *.trr" it is ok. <BR>> Hi all,<BR>>
<BR>> I use<BR>> > trjconv -f md.trr -s b4md.tpr -n index.ndx -o
md_500ps.trr -e 500<BR>> to extract 500ps trajectory from 1ns
trajectory.<BR>> <BR>> but I found the output trr file is only one
fourth of the original one.<BR>> <BR>> what is deleted when I use this
command?<BR>> <BR>> thanks for your reply in advance.<BR>> <BR>>
Regards,<BR>> <BR>> Jian Zou<BR>> <BR>>
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