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<DIV><FONT face=Arial size=2><SPAN class=815334302-22052006>Dear
all,</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=815334302-22052006>I want to to
calculate the diffusion coefficient of waters in hydration shell. I
searched the mailing list and found some relevent discussions about this. But I
can't get the clear solution about this yet.</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=815334302-22052006>My system includes 8
proteins ( res 1-1216) and H2O (res 1217-5258). According to the hints in
mailing list, I used:</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=815334302-22052006></SPAN></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=815334302-22052006>trjorder -f xxx.xtc -s xxx.tpr -n index.ndx -o
xxx_ordered.xtc (select protein as reference group and SOL as
molecules group which diffusion coefficient will be
calculated) </SPAN></FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=815334302-22052006>trjconv -f xxx_ordered.xtc -n index.ndx -o
xxx.gro</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=815334302-22052006></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=815334302-22052006>After these, I don't
know how to do next in order to get D in hydration shell.</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=815334302-22052006></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=815334302-22052006>So, could anybody
shed any light on my questions as follows:</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=815334302-22052006>1, how does trjorder
order the SOL molecules? </SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=815334302-22052006>I guess that
trjorder orders the SOL according to its distance to protein for every time
frame, i.e, the H2O which is the nearest to protein is labeled the 1st SOL (res
no. is 1217, in my case), the H2O which is the second nearest to protein is
labelled the 2nd SOL (res no. is 1218, in my case), and so on for every time
frame. Is it right? That means from the 1st time frame to 2nd frame, the H2O
molecules will be reordered, right?</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=815334302-22052006></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=815334302-22052006>2, After using
trjorder and trjconv, how to calculate D? I simply used xxx_ordered.xtc to
calculate D of water in hydration shell ( selected the first 1600 H2O molecules
according to the H2O number in the hydration shell guessed). But I found that
the result is too large to be reasonable. I guess that, from the first frame to
second frame, the molecules with the same labels (r1217, for example) are not
the same molecules because H2O molecules have been reordered. In this case, I
can not figure out how to achieve D.</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=815334302-22052006></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=815334302-22052006>Any suggesstion are
welcome. Thank you very much.</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=815334302-22052006></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=815334302-22052006>Hu
Zhongqiao</SPAN></FONT></DIV></BODY></HTML>