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<DIV><FONT face=Arial size=2><SPAN
class=047014203-21052007>Hi,</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=047014203-21052007></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=047014203-21052007>I faced one problem
when reading xtc file.</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=047014203-21052007></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=047014203-21052007>Assuming my xtc file
is run.xtc and the last frame no. is 10000 (time step=1ps, e.g, 10 ns in total),
I want to see the coordinates of the whole system without jump at frame=10000,
and I used the command:</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=047014203-21052007></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=047014203-21052007>(1)trjconv -f
run.xtc -s run.tpr -o sys_10000.pdb -b 10000 -e 10000 -pbc
nojump</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=047014203-21052007></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=047014203-21052007>That is no problem,
of course.</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=047014203-21052007></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=047014203-21052007>But I thought I
could also do the same thing by 2 steps as follows:</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=047014203-21052007></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=047014203-21052007>(2.1) first
convert run.xtc to run_nojump.xtc (using -pbc nojump)</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=047014203-21052007>trjconv -f
run.xtc -s run.tpr -o run_nojump.xtc -pbc nojump</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=047014203-21052007></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=047014203-21052007>(2.2) use trjconv
again to extract coordinates of system at frame=10000 from run_nojump.xtc (
I thought I didnt need to use flag -pbc nojump in this case)</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=047014203-21052007><SPAN
class=047014203-21052007>trjconv -f run_nojump.xtc -s run.tpr -o sys_10000.pdb
-b 10000 -e 10000</SPAN></SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=047014203-21052007><SPAN
class=047014203-21052007>But it is strange that some coordinates by 2 ways are
different. It seems that something wrong happened in step2.2 by checking the
coordinates.</SPAN></SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=047014203-21052007><SPAN
class=047014203-21052007></SPAN></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=047014203-21052007><SPAN
class=047014203-21052007>But when I add flag -pbc nojump for the step
2.2</SPAN></SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=047014203-21052007><SPAN
class=047014203-21052007><SPAN class=047014203-21052007><SPAN
class=047014203-21052007>trjconv -f run_nojump.xtc -s run.tpr -o sys_10000.pdb
-b 10000 -e 10000 -pbc nojump</SPAN></SPAN></SPAN></SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=047014203-21052007><SPAN
class=047014203-21052007><SPAN class=047014203-21052007><SPAN
class=047014203-21052007>It does work.</SPAN></SPAN></SPAN></SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=047014203-21052007><SPAN
class=047014203-21052007><SPAN class=047014203-21052007><SPAN
class=047014203-21052007></SPAN></SPAN></SPAN></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=047014203-21052007><SPAN
class=047014203-21052007>Did anyone meet the same problem and give a reasonable
explanation? </SPAN></SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=047014203-21052007><SPAN
class=047014203-21052007></SPAN></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=047014203-21052007><SPAN
class=047014203-21052007>In fact, I want to read coordinates of some particles
without jump to get the Mean Square Displacement (MSD). I used readxtc, a
Fortran Code, to get it, by linking xdr library, which is suggested by
Gromacs developers. But when readxtc read run_nojump.xtc, it can not give
the correct coordinates without jump, similar to what I said above. Then any
method to make a suitable xtc file which allow readxtc to get out
coordinates without jumps? Or after first coordinates with jump are read
out using readxtc, how can I convert them into those without jump in my
Fortran code?</SPAN></SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=047014203-21052007><SPAN
class=047014203-21052007></SPAN></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=047014203-21052007><SPAN
class=047014203-21052007>By the way, I need to extract coordinates of some
particles satisfying some specific conditions and these particle changes
from one frame to another frame, so some availabe analysis commands
cannot do this conveniently. </SPAN></SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=047014203-21052007><SPAN
class=047014203-21052007></SPAN></SPAN></FONT> </DIV>
<DIV><FONT face="Times New Roman" size=4>Zhongqiao Hu</FONT></DIV>
<DIV align=left>
<DIV align=left><FONT face=Arial size=2></FONT> </DIV></DIV>
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