<DIV>Yes. I should first run the 3x3x0.8 water to make the water </DIV>

<P sizset="31" sizcache="20">in <A class="blue12other" href="http://dict.youdao.com/search?q=equilibrium&amp;keyfrom=E2Ctranslation"><FONT color="#0022cc">equilibrium</FONT></A>. And then i use editconf to put the water at the centre of </P>

<P sizset="31" sizcache="20">3x3x9 box, so the film was 0.8 nm, the Z dimension is 9 nm, so there will be film.</P>

<P sizset="31" sizcache="20">I want to simulate the rupture of the thickness of water film. </P>

<P sizset="31" sizcache="20">&nbsp;</P>

<P sizset="31" sizcache="20">If i directly put the&nbsp; 3x3x0.8 water in the 3x3x9 box, i will try to see the result.</P>

<P sizset="31" sizcache="20">&nbsp;</P>

<P sizset="31" sizcache="20">I</P>

<DIV><BR>&nbsp;</DIV>

<DIV></DIV><BR><PRE><BR>At&nbsp;2010-12-17&nbsp;13:12:43，"Vitaly&nbsp;Chaban"&nbsp;&lt;vvchaban@gmail.com&gt;&nbsp;wrote:

&gt;I&nbsp;still&nbsp;do&nbsp;not&nbsp;understand&nbsp;what&nbsp;physical&nbsp;system&nbsp;you&nbsp;want&nbsp;to&nbsp;create&nbsp;in

&gt;the&nbsp;MD&nbsp;system&nbsp;or&nbsp;what&nbsp;phenomenon&nbsp;you&nbsp;want&nbsp;to&nbsp;reproduce.

&gt;

&gt;If&nbsp;you&nbsp;need&nbsp;a&nbsp;water&nbsp;film,&nbsp;then&nbsp;the&nbsp;only&nbsp;solution&nbsp;is&nbsp;to&nbsp;follow&nbsp;my

&gt;former&nbsp;suggestion.

&gt;

&gt;In&nbsp;no&nbsp;case&nbsp;should&nbsp;you&nbsp;use&nbsp;"3x3x0.8&nbsp;NPT"&nbsp;MD&nbsp;box!&nbsp;If&nbsp;somebody&nbsp;suggested

&gt;you&nbsp;to&nbsp;do&nbsp;such&nbsp;thing,&nbsp;then&nbsp;this&nbsp;person&nbsp;simply&nbsp;does&nbsp;not&nbsp;understand

&gt;classical&nbsp;MD&nbsp;simulations.

&gt;

&gt;--

&gt;Dr.Vitaly&nbsp;V.&nbsp;Chaban

&gt;

&gt;

&gt;

&gt;

&gt;

&gt;

&gt;On&nbsp;Thu,&nbsp;Dec&nbsp;16,&nbsp;2010&nbsp;at&nbsp;11:48&nbsp;PM,&nbsp;gromacs&nbsp;&lt;ptf1242@163.com&gt;&nbsp;wrote:

&gt;&gt;&nbsp;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.

&gt;&gt;

&gt;&gt;&nbsp;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.

&gt;&gt;&nbsp;At&nbsp;2010-12-17&nbsp;09:51:57，"Vitaly&nbsp;Chaban"&nbsp;&lt;vvchaban@gmail.com&gt;&nbsp;wrote:

&gt;&gt;&gt;&gt;&gt;Hey,&nbsp;gromacs&nbsp;-

&gt;&gt;&gt;&gt;&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;&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;&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;&gt;&gt;z-side.

&gt;&gt;&gt;&gt;&gt;

&gt;&gt;&gt;&gt;&gt;--

&gt;&gt;&gt;&gt;&gt;Dr.&nbsp;Vitaly&nbsp;V.&nbsp;Chaban

&gt;&gt;&gt;&gt;&gt;Rochester,&nbsp;U.S.A.

&gt;&gt;&gt;&gt;&gt;

&gt;&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;

&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;

&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;

&gt;&gt;&gt;

&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;&gt;&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;&gt;&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;&gt;&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;&gt;

&gt;&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;&gt;&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;&gt;&gt;of&nbsp;water&nbsp;and&nbsp;apply&nbsp;editconf&nbsp;-

&gt;&gt;&gt;

&gt;&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;&gt;

&gt;&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;&gt;&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;&gt;&gt;center&nbsp;surrounded&nbsp;by&nbsp;vacuum&nbsp;in&nbsp;one&nbsp;(Z)&nbsp;direction.

&gt;&gt;&gt;

&gt;&gt;&gt;Happy&nbsp;GROMACSing,

&gt;&gt;&gt;

&gt;&gt;&gt;Dr.&nbsp;Vitaly&nbsp;V.&nbsp;Chaban

&gt;&gt;&gt;Rochester,&nbsp;U.S.A.

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