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<DIV>Hi&nbsp;all</DIV>

<DIV>&nbsp;</DIV>

<DIV></DIV>

<DIV>In&nbsp;GMX4&nbsp;paper&nbsp;</DIV>

<DIV>"GROMACS&nbsp;4:&nbsp;Algorithms&nbsp;for&nbsp;Highly&nbsp;Efficient,&nbsp;Load-Balanced,&nbsp;and&nbsp;Scalable&nbsp;Molecular&nbsp;Simulation"&nbsp;</DIV>

<DIV>&nbsp;</DIV>

<DIV>VIII.&nbsp;Other&nbsp;New&nbsp;Features.&nbsp;It&nbsp;says&nbsp;that</DIV>

<DIV>"Previously,&nbsp;GROMACS&nbsp;only&nbsp;supported&nbsp;neighbor&nbsp;list&nbsp;updates</DIV>

<DIV>at&nbsp;fixed&nbsp;intervals,&nbsp;but&nbsp;the&nbsp;use&nbsp;of&nbsp;potentials&nbsp;that&nbsp;are&nbsp;switched</DIV>

<DIV>exactly&nbsp;to&nbsp;zero&nbsp;at&nbsp;some&nbsp;finite&nbsp;distance&nbsp;is&nbsp;increasing,&nbsp;mainly</DIV>

<DIV>to&nbsp;avoid&nbsp;cutoff&nbsp;effects.&nbsp;To&nbsp;be&nbsp;sure&nbsp;that&nbsp;no&nbsp;interaction&nbsp;is</DIV>

<DIV>missed,&nbsp;the&nbsp;neighbor&nbsp;list&nbsp;can&nbsp;be&nbsp;updated&nbsp;heuristically&nbsp;in</DIV>

<DIV>"ROMACS&nbsp;4.</DIV>

<DIV>&nbsp;</DIV>

<DIV></DIV>

<DIV>And&nbsp;in&nbsp;IX.&nbsp;Benchmarks</DIV>

<DIV>It&nbsp;says&nbsp;that&nbsp;"The&nbsp;neighbor&nbsp;list&nbsp;was&nbsp;updated&nbsp;heuristically&nbsp;with&nbsp;a&nbsp;buffer&nbsp;of 

0.26&nbsp;nm."</DIV>

<DIV>&nbsp;</DIV>

<DIV></DIV>

<DIV>But&nbsp;I&nbsp;don't&nbsp;known&nbsp;how&nbsp;to&nbsp;set&nbsp;the&nbsp;buffer&nbsp;size&nbsp;in&nbsp;the&nbsp;*.mdp&nbsp;file.&nbsp;Can&nbsp;someone&nbsp;give&nbsp;me&nbsp;an&nbsp;idea?</DIV>

<DIV>&nbsp;</DIV>

<DIV>Appreciate&nbsp;any&nbsp;help&nbsp;in&nbsp;advance!</DIV>

<DIV></DIV>

<DIV>&nbsp;</DIV></FONT></DIV>

<DIV><FONT face=Verdana size=2></FONT>&nbsp;</DIV>

<DIV align=left><FONT face=Verdana color=#c0c0c0 size=2>2010-06-17 

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<DIV>&nbsp;</DIV>

<DIV>Best </DIV>

<DIV>&nbsp;&nbsp;&nbsp; wishes&#65281;</DIV>

<DIV>&nbsp;</DIV>

<DIV>Ji Xu</DIV>

<DIV></DIV>

<DIV>The&nbsp;State&nbsp;Key&nbsp;Laboratory&nbsp;of&nbsp;Multiphase&nbsp;Complex&nbsp;System</DIV>

<DIV>Institute&nbsp;of&nbsp;Process&nbsp;Engineering</DIV>

<DIV>Chinese&nbsp;Academy&nbsp;of&nbsp;Sciences</DIV>

<DIV>Beijing&nbsp;100190,&nbsp;China</DIV>

<DIV>Tel.:&nbsp;+86&nbsp;10&nbsp;8262&nbsp;3713-804&nbsp;</DIV></DIV></DIV></SPAN></FONT></DIV></FONT></BODY></HTML>