<div style="line-height:1.7;color:#000000;font-size:14px;font-family:arial"><div>Yes, i try to get a surface tension of 69 dyn, but i can only get 65 at present. </div><div id="isForwardContent"><div style="color: rgb(0, 0, 0); line-height: 1.7; font-family: arial; font-size: 14px;"><div>&nbsp;</div><div>Yes, i tried some arbitrary choices. I do not know what is the correct .mdp for me to get a surface tension of 69. May be for this version, it does not include this function</div><div>&nbsp;</div><div>Thanks for your kind message. But i still does not how to figure it out.</div><div>&nbsp;</div><div>&nbsp;</div><div></div><div></div><pre><br>At&nbsp;2012-05-30&nbsp;15:43:36,<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>&nbsp;wrote:
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&gt;
&gt;Today's&nbsp;Topics:
&gt;
&gt;&nbsp;&nbsp;&nbsp;1.&nbsp;can&nbsp;Gromacs&nbsp;4.5&nbsp;use&nbsp;VDW&nbsp;long&nbsp;range&nbsp;correction?&nbsp;IN&nbsp;the
&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;mannual,&nbsp;In&nbsp;this&nbsp;version,&nbsp;GROMACS&nbsp;always&nbsp;uses&nbsp;a&nbsp;cut-off&nbsp;radius
&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;for&nbsp;the&nbsp;Lennard-Jones&nbsp;interactions&nbsp;(MD)
&gt;&nbsp;&nbsp;&nbsp;2.&nbsp;Re:&nbsp;can&nbsp;Gromacs&nbsp;4.5&nbsp;use&nbsp;VDW&nbsp;long&nbsp;range&nbsp;correction?&nbsp;IN        the
&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;mannual,&nbsp;In&nbsp;this&nbsp;version,        GROMACS&nbsp;always&nbsp;uses&nbsp;a&nbsp;cut-off&nbsp;radius
&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;for&nbsp;the        Lennard-Jones&nbsp;interactions&nbsp;(Mark&nbsp;Abraham)
&gt;
&gt;
&gt;----------------------------------------------------------------------
&gt;
&gt;Message:&nbsp;1
&gt;Date:&nbsp;Wed,&nbsp;30&nbsp;May&nbsp;2012&nbsp;15:33:53&nbsp;+0800&nbsp;(CST)
&gt;From:&nbsp;MD&nbsp;&nbsp;&lt;<a href="mailto:ptf1242@163.com">ptf1242@163.com</a>&gt;
&gt;Subject:&nbsp;[gmx-users]&nbsp;can&nbsp;Gromacs&nbsp;4.5&nbsp;use&nbsp;VDW&nbsp;long&nbsp;range&nbsp;correction?&nbsp;IN
&gt;        the&nbsp;mannual,&nbsp;In&nbsp;this&nbsp;version,&nbsp;GROMACS&nbsp;always&nbsp;uses&nbsp;a&nbsp;cut-off&nbsp;radius&nbsp;for
&gt;        the&nbsp;Lennard-Jones&nbsp;interactions
&gt;To:&nbsp;<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
&gt;Message-ID:&nbsp;&lt;<a href="mailto:1dc9ba2d.c95b.1379caa467e.Coremail.ptf1242@163.com">1dc9ba2d.c95b.1379caa467e.Coremail.ptf1242@163.com</a>&gt;
&gt;Content-Type:&nbsp;text/plain;&nbsp;charset="gbk"
&gt;
&gt;Hi&nbsp;All,
&gt;&nbsp;
&gt;I&nbsp;have&nbsp;to&nbsp;use&nbsp;the&nbsp;long&nbsp;range&nbsp;correction&nbsp;for&nbsp;VDW,&nbsp;in&nbsp;fact&nbsp;i&nbsp;used&nbsp;cut-off=1.4&nbsp;nm&nbsp;for&nbsp;calculation&nbsp;of&nbsp;surface&nbsp;tension&nbsp;of&nbsp;TIP4P/2005,&nbsp;we&nbsp;can&nbsp;get&nbsp;65&nbsp;dyn.&nbsp;The&nbsp;.mdp&nbsp;i&nbsp;used&nbsp;are&nbsp;as&nbsp;follow,&nbsp;I&nbsp;really&nbsp;need&nbsp;to&nbsp;know&nbsp;how&nbsp;to&nbsp;get&nbsp;a&nbsp;surface&nbsp;tension&nbsp;of&nbsp;69.5&nbsp;dyn&nbsp;for&nbsp;TIP4P/2005&nbsp;water&nbsp;model.&nbsp;Becasue&nbsp;my&nbsp;surpervisor&nbsp;is&nbsp;so&nbsp;picky,&nbsp;everything&nbsp;should&nbsp;be&nbsp;perfacet,&nbsp;and&nbsp;i&nbsp;feel&nbsp;really&nbsp;tired&nbsp;by&nbsp;his&nbsp;way.&nbsp;Any&nbsp;comment&nbsp;will&nbsp;be&nbsp;greatly&nbsp;appreciated,
&gt;&nbsp;
&gt;The&nbsp;main&nbsp;parameter&nbsp;is
&gt;&nbsp;
&gt;
&gt;coulombtype&nbsp;=&nbsp;PME
&gt;
&gt;rcoulomb-switch&nbsp;=&nbsp;0
&gt;
&gt;rcoulomb&nbsp;=&nbsp;1.4
&gt;
&gt;;&nbsp;Dielectric&nbsp;constant&nbsp;(DC)&nbsp;for&nbsp;cut-off&nbsp;or&nbsp;DC&nbsp;of&nbsp;reaction&nbsp;field
&gt;
&gt;epsilon-r&nbsp;=&nbsp;1
&gt;
&gt;;&nbsp;Method&nbsp;for&nbsp;doing&nbsp;Van&nbsp;der&nbsp;Waals
&gt;
&gt;vdw-type&nbsp;=&nbsp;Cut-off
&gt;
&gt;;&nbsp;cut-off&nbsp;lengths
&gt;
&gt;rvdw-switch&nbsp;=&nbsp;0
&gt;
&gt;rvdw&nbsp;=&nbsp;3.8
&gt;
&gt;;&nbsp;Apply&nbsp;long&nbsp;range&nbsp;dispersion&nbsp;corrections&nbsp;for&nbsp;Energy&nbsp;and&nbsp;Pressure
&gt;
&gt;DispCorr&nbsp;=&nbsp;EnerPres
&gt;
&gt;;&nbsp;Extension&nbsp;of&nbsp;the&nbsp;potential&nbsp;lookup&nbsp;tables&nbsp;beyond&nbsp;the&nbsp;cut-off
&gt;
&gt;table-extension&nbsp;=&nbsp;1
&gt;
&gt;;&nbsp;Spacing&nbsp;for&nbsp;the&nbsp;PME/PPPM&nbsp;FFT&nbsp;grid
&gt;
&gt;fourierspacing&nbsp;=&nbsp;0.12
&gt;
&gt;&nbsp;

&gt;
&gt;Message:&nbsp;2
&gt;Date:&nbsp;Wed,&nbsp;30&nbsp;May&nbsp;2012&nbsp;17:42:57&nbsp;+1000
&gt;From:&nbsp;Mark&nbsp;Abraham&nbsp;&lt;<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>&gt;
&gt;Subject:&nbsp;Re:&nbsp;[gmx-users]&nbsp;can&nbsp;Gromacs&nbsp;4.5&nbsp;use&nbsp;VDW&nbsp;long&nbsp;range
&gt;        correction?&nbsp;IN        the&nbsp;mannual,&nbsp;In&nbsp;this&nbsp;version,        GROMACS&nbsp;always&nbsp;uses&nbsp;a
&gt;        cut-off&nbsp;radius&nbsp;for&nbsp;the        Lennard-Jones&nbsp;interactions
&gt;To:&nbsp;Discussion&nbsp;list&nbsp;for&nbsp;GROMACS&nbsp;users&nbsp;&lt;<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>&gt;
&gt;Message-ID:&nbsp;&lt;<a href="mailto:4FC5CF81.7000203@anu.edu.au">4FC5CF81.7000203@anu.edu.au</a>&gt;
&gt;Content-Type:&nbsp;text/plain;&nbsp;charset="iso-8859-1"
&gt;
&gt;On&nbsp;30/05/2012&nbsp;5:33&nbsp;PM,&nbsp;MD&nbsp;wrote:
&gt;&gt;&nbsp;Hi&nbsp;All,
&gt;&gt;&nbsp;I&nbsp;have&nbsp;to&nbsp;use&nbsp;the&nbsp;long&nbsp;range&nbsp;correction&nbsp;for&nbsp;VDW,&nbsp;in&nbsp;fact&nbsp;i&nbsp;used&nbsp;
&gt;&gt;&nbsp;cut-off=1.4&nbsp;nm&nbsp;for&nbsp;calculation&nbsp;of&nbsp;surface&nbsp;tension&nbsp;of&nbsp;TIP4P/2005,&nbsp;we&nbsp;
&gt;&gt;&nbsp;can&nbsp;get&nbsp;65&nbsp;dyn.&nbsp;The&nbsp;.mdp&nbsp;i&nbsp;used&nbsp;are&nbsp;as&nbsp;follow,&nbsp;I&nbsp;really&nbsp;need&nbsp;to&nbsp;know&nbsp;
&gt;&gt;&nbsp;how&nbsp;to&nbsp;get&nbsp;a&nbsp;surface&nbsp;tension&nbsp;of&nbsp;69.5&nbsp;dyn&nbsp;for&nbsp;TIP4P/2005&nbsp;water&nbsp;model.
&gt;
&gt;By&nbsp;finding&nbsp;the&nbsp;method&nbsp;that&nbsp;was&nbsp;used&nbsp;then&nbsp;and&nbsp;attempting&nbsp;to&nbsp;replicate&nbsp;it?
&gt;
&gt;&gt;&nbsp;Becasue&nbsp;my&nbsp;surpervisor&nbsp;is&nbsp;so&nbsp;picky,&nbsp;everything&nbsp;should&nbsp;be&nbsp;perfacet,&nbsp;and&nbsp;
&gt;&gt;&nbsp;i&nbsp;feel&nbsp;really&nbsp;tired&nbsp;by&nbsp;his&nbsp;way.&nbsp;Any&nbsp;comment&nbsp;will&nbsp;be&nbsp;greatly&nbsp;appreciated,
&gt;
&gt;A&nbsp;certain&nbsp;degree&nbsp;of&nbsp;pickiness&nbsp;is&nbsp;essential.&nbsp;You're&nbsp;apparently&nbsp;trying&nbsp;to&nbsp;
&gt;replicate&nbsp;a&nbsp;result&nbsp;by&nbsp;making&nbsp;some&nbsp;arbitrary&nbsp;choices.&nbsp;Don't.
&gt;
&gt;This&nbsp;.mdp&nbsp;file&nbsp;generates&nbsp;velocities,&nbsp;thus&nbsp;did&nbsp;not&nbsp;start&nbsp;in&nbsp;an&nbsp;
&gt;equilibrium&nbsp;ensemble.&nbsp;However&nbsp;you&nbsp;measured&nbsp;your&nbsp;surface&nbsp;tension&nbsp;needs&nbsp;to&nbsp;
&gt;exclude&nbsp;the&nbsp;equilibration&nbsp;time.
&gt;
&gt;Mark
</pre></div><br><span title="neteasefooter"><span id="netease_mail_footer"></span></span></div></div><br><br><span title="neteasefooter"><span id="netease_mail_footer"></span></span>