<PRE><BR></PRE>
<P>--------&nbsp;Forwarding&nbsp;messages&nbsp;--------
From:&nbsp;gromacs&nbsp;&lt;ptf1242@163.com&gt;
Date:&nbsp;2010-12-17&nbsp;12:48:55To:&nbsp;&nbsp;vvchaban@gmail.com
Cc:&nbsp;&nbsp;gmx-users@gromacs.org
Subject:&nbsp;Re:Re:&nbsp;water&nbsp;genbox&nbsp;3x3x0.8&nbsp;EM&nbsp;not&nbsp;successful&nbsp;T&nbsp;not&nbsp;high
OK.&nbsp;I&nbsp;will&nbsp;use&nbsp;your&nbsp;method.&nbsp;But&nbsp;i&nbsp;am&nbsp;afraid&nbsp;there&nbsp;will&nbsp;be&nbsp;something&nbsp;wrong.&nbsp;Because&nbsp;generally,&nbsp;i&nbsp;should&nbsp;run&nbsp;the&nbsp;3x3x0.8&nbsp;NPT&nbsp;water,&nbsp;and&nbsp;then&nbsp;i&nbsp;use&nbsp;editconf&nbsp;to&nbsp;add&nbsp;the&nbsp;water&nbsp;to&nbsp;3x3x3.&nbsp;If&nbsp;i&nbsp;donot&nbsp;run&nbsp;3x3x0.8,&nbsp;i&nbsp;may&nbsp;not&nbsp;be&nbsp;able&nbsp;to&nbsp;run&nbsp;the&nbsp;final&nbsp;interface&nbsp;box.&nbsp;Because&nbsp;the&nbsp;water&nbsp;in&nbsp;the&nbsp;box&nbsp;is&nbsp;not&nbsp;at&nbsp;proper&nbsp;situation&nbsp;or&nbsp;position.&nbsp;Anyway,&nbsp;i&nbsp;will&nbsp;have&nbsp;a&nbsp;try&nbsp;first.
</P>
<P>One problem is that how can i make the Energy Minimising successful?</P>
<P>There are some water molecules not in suitable position.&nbsp;</P>
<P>
If&nbsp;i&nbsp;have&nbsp;problem&nbsp;or&nbsp;success,&nbsp;i&nbsp;will&nbsp;give&nbsp;an&nbsp;answer&nbsp;to&nbsp;all.
At&nbsp;2010-12-17&nbsp;09:51:57£¬"Vitaly&nbsp;Chaban"&nbsp;&lt;vvchaban@gmail.com&gt;&nbsp;wrote:
&gt;&gt;&gt;Hey,&nbsp;gromacs&nbsp;-&gt;&gt;&gt;
&gt;&gt;&gt;Nice&nbsp;to&nbsp;hear&nbsp;from&nbsp;you&nbsp;here...&nbsp;It&nbsp;is&nbsp;a&nbsp;bad&nbsp;idea&nbsp;to&nbsp;simulate&nbsp;something
&gt;&gt;&gt;with&nbsp;any&nbsp;cartesian&nbsp;dimension&nbsp;lower&nbsp;than&nbsp;a&nbsp;couple&nbsp;of&nbsp;nanometers&nbsp;using
&gt;&gt;&gt;classical&nbsp;FFs.&nbsp;&nbsp;All&nbsp;your&nbsp;problems&nbsp;are&nbsp;generated&nbsp;by&nbsp;0.8&nbsp;nm&nbsp;of&nbsp;the
&gt;&gt;&gt;z-side.&gt;&gt;&gt;&gt;&gt;&gt;--
&gt;&gt;&gt;Dr.&nbsp;Vitaly&nbsp;V.&nbsp;Chaban
&gt;&gt;&gt;Rochester,&nbsp;U.S.A.&gt;&gt;&gt;&gt;&gt;
&gt;&gt;&nbsp;Thanks&nbsp;very&nbsp;much.&nbsp;I&nbsp;use&nbsp;the&nbsp;cutoff=0.38,&nbsp;because&nbsp;the&nbsp;cutoff&nbsp;should&nbsp;be&nbsp;smaller&nbsp;than&nbsp;the&nbsp;half&nbsp;box&nbsp;size.&nbsp;I&nbsp;guess&nbsp;it&nbsp;may&nbsp;be&nbsp;the&nbsp;Z&nbsp;dimension&nbsp;is&nbsp;too&nbsp;small,&nbsp;Plus&nbsp;the&nbsp;PBC.&nbsp;But&nbsp;when&nbsp;i&nbsp;use&nbsp;1.8x1.8x1.8nm&nbsp;bulk&nbsp;water,&nbsp;all&nbsp;results&nbsp;are&nbsp;OK.
&gt;&gt;
&gt;&gt;&nbsp;My&nbsp;teacher&nbsp;wants&nbsp;me&nbsp;to&nbsp;simulate&nbsp;3x3x0.8,&nbsp;3x3x0.9&nbsp;nm&nbsp;water&nbsp;film's&nbsp;rupture.&nbsp;So&nbsp;i&nbsp;have&nbsp;to&nbsp;run&nbsp;bulk&nbsp;&gt;3x3x0.8&nbsp;water&nbsp;and&nbsp;then&nbsp;add&nbsp;box&nbsp;to&nbsp;3x3x9&nbsp;to&nbsp;form&nbsp;interface.
&gt;&gt;
&gt;&gt;&nbsp;So&nbsp;if&nbsp;i&nbsp;want&nbsp;to&nbsp;run&nbsp;run&nbsp;bulk&nbsp;3x3x0.8&nbsp;water,&nbsp;how&nbsp;could&nbsp;i&nbsp;do?&nbsp;which&nbsp;FF&nbsp;should&nbsp;i&nbsp;use?&nbsp;the&nbsp;high&nbsp;T&nbsp;may&nbsp;be&nbsp;&gt;due&nbsp;to&nbsp;EM&nbsp;not&nbsp;success??
&gt;&gt;
&gt;I&nbsp;believe&nbsp;you&nbsp;use&nbsp;the&nbsp;term&nbsp;"bulk&nbsp;water"&nbsp;in&nbsp;another&nbsp;sense&nbsp;as&nbsp;compared
&gt;to&nbsp;all&nbsp;other&nbsp;guys&nbsp;here.&nbsp;When&nbsp;people&nbsp;say&nbsp;"bulk&nbsp;liquid"&nbsp;they&nbsp;imply&nbsp;the
&gt;endless&nbsp;ocean&nbsp;of&nbsp;this&nbsp;liquid.&nbsp;It&nbsp;is&nbsp;not&nbsp;important&nbsp;what&nbsp;particular&nbsp;side
&gt;lengths&nbsp;you&nbsp;have,&nbsp;since&nbsp;due&nbsp;to&nbsp;PBC&nbsp;you&nbsp;get&nbsp;infinitively&nbsp;large&nbsp;system.
&gt;
&gt;I&nbsp;suspect&nbsp;your&nbsp;teacher&nbsp;wants&nbsp;you&nbsp;to&nbsp;obtain&nbsp;a&nbsp;film&nbsp;of&nbsp;water&nbsp;that&nbsp;would
&gt;be&nbsp;about&nbsp;3&nbsp;molecular&nbsp;layers&nbsp;wide.&nbsp;That's&nbsp;easy.&nbsp;Take&nbsp;your&nbsp;current&nbsp;box
&gt;of&nbsp;water&nbsp;and&nbsp;apply&nbsp;editconf&nbsp;-&gt;
&gt;editconf&nbsp;-f&nbsp;&lt;current_conf&gt;&nbsp;-o&nbsp;&lt;water_film_conf&gt;&nbsp;-box&nbsp;3&nbsp;3&nbsp;3
&gt;
&gt;Finally,&nbsp;just&nbsp;start&nbsp;MD&nbsp;run&nbsp;with&nbsp;a&nbsp;water_film_conf.&nbsp;You'll&nbsp;have&nbsp;the
&gt;same&nbsp;periodic&nbsp;box&nbsp;,&nbsp;but&nbsp;water&nbsp;molecules&nbsp;will&nbsp;be&nbsp;present&nbsp;only&nbsp;at&nbsp;its
&gt;center&nbsp;surrounded&nbsp;by&nbsp;vacuum&nbsp;in&nbsp;one&nbsp;(Z)&nbsp;direction.
&gt;&gt;Happy&nbsp;GROMACSing,&gt;&gt;Dr.&nbsp;Vitaly&nbsp;V.&nbsp;Chaban
&gt;Rochester,&nbsp;U.S.A.</P><br><br><span title="neteasefooter"><span id="netease_mail_footer"></span></span>