<DIV>Sorry, i write wrong.</DIV>

<DIV>&nbsp;</DIV>

<DIV>Someone&nbsp;said&nbsp;that&nbsp;we&nbsp;cannot&nbsp;get&nbsp;sufactant.gro&nbsp;and&nbsp;sufactant.top&nbsp;through&nbsp;pdb2gmx()&nbsp;&nbsp;sufactant.pdb.&nbsp;Because&nbsp;grompp&nbsp;&nbsp;.pdb&nbsp;could&nbsp;mainly&nbsp;use&nbsp;for&nbsp;macro-biology&nbsp;big&nbsp;moleculars,&nbsp;which&nbsp;means&nbsp;some&nbsp;proteins&nbsp;etc.</DIV>

<DIV>&nbsp;</DIV>

<DIV>&nbsp;So&nbsp;that&nbsp;means&nbsp;we&nbsp;could&nbsp;not&nbsp;get&nbsp;correct&nbsp;&nbsp;.gro,&nbsp;.top&nbsp;small&nbsp;molecules&nbsp;such&nbsp;as&nbsp;inorganic&nbsp;or&nbsp;small&nbsp;organic&nbsp;molecules&nbsp;(such&nbsp;as&nbsp;ethanol) by using pdb2max command. </DIV>

<DIV>&nbsp;</DIV>

<DIV>Maybe we could get get sufactant.gro, sufactant.top through the following? <A title="Downloads/Related Software/SwissParam" href="http://www.gromacs.org/Downloads/Related_Software/SwissParam" rel="internal">SwissParam</A> (for CHARMM forcefield), <A title="Documentation/Commands/PRODRG" href="http://www.gromacs.org/Downloads/Related_Software/PRODRG" rel="internal">PRODRG</A>&nbsp;(for ffgmx/GROMOS96 43A1), <A title="Downloads/Related Software/Automated Topology Builder" href="http://www.gromacs.org/Downloads/Related_Software/Automated_Topology_Builder" rel="internal">Automated Topology Builder</A> (for GROMOS96 53A6),&nbsp;<A title="Documentation/Commands/MKTOP" href="http://www.gromacs.org/Downloads/Related_Software/MKTOP" rel="internal">MKTOP</A> (for OPLS/AA)<BR>?</DIV>

<DIV>But how can we get surfactant such as SDS .gro?<BR><BR></DIV>

<DIV></DIV><BR><PRE><BR>At&nbsp;2011-01-04&nbsp;16:19:05，gmx-users-request@gromacs.org&nbsp;wrote:

&gt;Send&nbsp;gmx-users&nbsp;mailing&nbsp;list&nbsp;submissions&nbsp;to

&gt;        gmx-users@gromacs.org

&gt;

&gt;To&nbsp;subscribe&nbsp;or&nbsp;unsubscribe&nbsp;via&nbsp;the&nbsp;World&nbsp;Wide&nbsp;Web,&nbsp;visit

&gt;        http://lists.gromacs.org/mailman/listinfo/gmx-users

&gt;or,&nbsp;via&nbsp;email,&nbsp;send&nbsp;a&nbsp;message&nbsp;with&nbsp;subject&nbsp;or&nbsp;body&nbsp;'help'&nbsp;to

&gt;        gmx-users-request@gromacs.org

&gt;

&gt;You&nbsp;can&nbsp;reach&nbsp;the&nbsp;person&nbsp;managing&nbsp;the&nbsp;list&nbsp;at

&gt;        gmx-users-owner@gromacs.org

&gt;

&gt;When&nbsp;replying,&nbsp;please&nbsp;edit&nbsp;your&nbsp;Subject&nbsp;line&nbsp;so&nbsp;it&nbsp;is&nbsp;more&nbsp;specific

&gt;than&nbsp;"Re:&nbsp;Contents&nbsp;of&nbsp;gmx-users&nbsp;digest..."

&gt;

&gt;

&gt;Today's&nbsp;Topics:

&gt;

&gt;&nbsp;&nbsp;&nbsp;1.&nbsp;Re:&nbsp;Re:&nbsp;[gmx-users]&nbsp;Trifluoroethanol-Ethanol&nbsp;mixtures&nbsp;study

&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(wibke.sudholt@cloudbroker.com)

&gt;&nbsp;&nbsp;&nbsp;2.&nbsp;Email&nbsp;bounce&nbsp;message&nbsp;(Mark&nbsp;Abraham)

&gt;&nbsp;&nbsp;&nbsp;3.&nbsp;g_mindist&nbsp;(Ramachandran&nbsp;G)

&gt;&nbsp;&nbsp;&nbsp;4.&nbsp;Re:&nbsp;g_mindist&nbsp;(Justin&nbsp;A.&nbsp;Lemkul)

&gt;&nbsp;&nbsp;&nbsp;5.&nbsp;Re:&nbsp;The&nbsp;sum&nbsp;of&nbsp;the&nbsp;O-H&nbsp;distancesof&nbsp;the&nbsp;backbone&nbsp;hydrogen

&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;bonds&nbsp;ROH&nbsp;(sreelakshmi&nbsp;ramesh)

&gt;&nbsp;&nbsp;&nbsp;6.&nbsp;How&nbsp;to&nbsp;get&nbsp;sufactant.gro,&nbsp;sufactant.top,&nbsp;(gromacs)

&gt;&nbsp;&nbsp;&nbsp;7.&nbsp;Re:&nbsp;How&nbsp;to&nbsp;get&nbsp;sufactant.gro,&nbsp;sufactant.top,&nbsp;(Mark&nbsp;Abraham)

&gt;

&gt;

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

&gt;

&gt;Message:&nbsp;1

&gt;Date:&nbsp;4&nbsp;Jan&nbsp;2011&nbsp;01:23:06&nbsp;+0100

&gt;From:&nbsp;wibke.sudholt@cloudbroker.com

&gt;Subject:&nbsp;Re:&nbsp;Re:&nbsp;[gmx-users]&nbsp;Trifluoroethanol-Ethanol&nbsp;mixtures&nbsp;study

&gt;To:&nbsp;gmx-users@gromacs.org

&gt;Message-ID:&nbsp;&lt;20110104002306.1761.qmail@server12.hostfactory.ch&gt;

&gt;Content-Type:&nbsp;text/plain;&nbsp;charset="UTF-8"

&gt;

&gt;Dear&nbsp;Email&nbsp;Sender,

&gt;

&gt;Thank&nbsp;you&nbsp;very&nbsp;much&nbsp;for&nbsp;contacting&nbsp;me!&nbsp;Unfortunately,&nbsp;I&nbsp;am&nbsp;not&nbsp;available&nbsp;in&nbsp;the&nbsp;office&nbsp;at&nbsp;the&nbsp;moment&nbsp;and&nbsp;cannot&nbsp;respond&nbsp;to&nbsp;your&nbsp;email.&nbsp;I&nbsp;will&nbsp;be&nbsp;able&nbsp;to&nbsp;handle&nbsp;your&nbsp;request&nbsp;starting&nbsp;again&nbsp;Monday,&nbsp;January&nbsp;10,&nbsp;2011.

&gt;

&gt;For&nbsp;all&nbsp;questions&nbsp;about&nbsp;CloudBroker,&nbsp;please&nbsp;contact&nbsp;the&nbsp;company&nbsp;under&nbsp;info@cloudbroker.com.&nbsp;In&nbsp;case&nbsp;you&nbsp;have&nbsp;any&nbsp;issues&nbsp;with&nbsp;the&nbsp;CloudBroker&nbsp;Platform,&nbsp;please&nbsp;send&nbsp;an&nbsp;email&nbsp;to&nbsp;our&nbsp;helpdesk&nbsp;at&nbsp;platform@cloudbroker.com.&nbsp;If&nbsp;you&nbsp;need&nbsp;to&nbsp;talk&nbsp;to&nbsp;me&nbsp;in&nbsp;person&nbsp;for&nbsp;urgent&nbsp;or&nbsp;important&nbsp;issues,&nbsp;please&nbsp;call&nbsp;my&nbsp;mobile&nbsp;phone&nbsp;number.

&gt;

&gt;Kind&nbsp;regards,

&gt;

&gt;Wibke&nbsp;Sudholt

&gt;

&gt;

&gt;--&nbsp;

&gt;Dr.&nbsp;Wibke&nbsp;Sudholt

&gt;Associate&nbsp;and&nbsp;Chair&nbsp;of&nbsp;the&nbsp;Management

&gt;CloudBroker&nbsp;GmbH

&gt;Technoparkstrasse&nbsp;1

&gt;CH-8005&nbsp;Zurich

&gt;Switzerland

&gt;Phone:&nbsp;+41&nbsp;44&nbsp;633&nbsp;79&nbsp;34

&gt;Email:&nbsp;&nbsp;info@cloudbroker.com

&gt;Web:&nbsp;&nbsp;&nbsp;&nbsp;http://www.cloudbroker.com

&gt;

&gt;

&gt;

&gt;

&gt;

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

&gt;

&gt;Message:&nbsp;2

&gt;Date:&nbsp;Tue,&nbsp;04&nbsp;Jan&nbsp;2011&nbsp;11:27:29&nbsp;+1100

&gt;From:&nbsp;Mark&nbsp;Abraham&nbsp;&lt;Mark.Abraham@anu.edu.au&gt;

&gt;Subject:&nbsp;[gmx-users]&nbsp;Email&nbsp;bounce&nbsp;message

&gt;To:&nbsp;Discussion&nbsp;list&nbsp;for&nbsp;GROMACS&nbsp;users&nbsp;&lt;gmx-users@gromacs.org&gt;

&gt;Message-ID:&nbsp;&lt;4D226971.8000808@anu.edu.au&gt;

&gt;Content-Type:&nbsp;text/plain;&nbsp;charset=UTF-8;&nbsp;format=flowed

&gt;

&gt;On&nbsp;4/01/2011&nbsp;11:23&nbsp;AM,&nbsp;wibke.sudholt@cloudbroker.com&nbsp;wrote:

&gt;&gt;&nbsp;Dear&nbsp;Email&nbsp;Sender,

&gt;&gt;

&gt;&gt;&nbsp;Thank&nbsp;you&nbsp;very&nbsp;much&nbsp;for&nbsp;contacting&nbsp;me!&nbsp;Unfortunately,&nbsp;I&nbsp;am&nbsp;not&nbsp;available&nbsp;in&nbsp;the&nbsp;office&nbsp;at&nbsp;the&nbsp;moment&nbsp;and&nbsp;cannot&nbsp;respond&nbsp;to&nbsp;your&nbsp;email.&nbsp;I&nbsp;will&nbsp;be&nbsp;able&nbsp;to&nbsp;handle&nbsp;your&nbsp;request&nbsp;starting&nbsp;again&nbsp;Monday,&nbsp;January&nbsp;10,&nbsp;2011.

&gt;&gt;

&gt;&gt;&nbsp;For&nbsp;all&nbsp;questions&nbsp;about&nbsp;CloudBroker,&nbsp;please&nbsp;contact&nbsp;the&nbsp;company&nbsp;under&nbsp;info@cloudbroker.com.&nbsp;In&nbsp;case&nbsp;you&nbsp;have&nbsp;any&nbsp;issues&nbsp;with&nbsp;the&nbsp;CloudBroker&nbsp;Platform,&nbsp;please&nbsp;send&nbsp;an&nbsp;email&nbsp;to&nbsp;our&nbsp;helpdesk&nbsp;at&nbsp;platform@cloudbroker.com.&nbsp;If&nbsp;you&nbsp;need&nbsp;to&nbsp;talk&nbsp;to&nbsp;me&nbsp;in&nbsp;person&nbsp;for&nbsp;urgent&nbsp;or&nbsp;important&nbsp;issues,&nbsp;please&nbsp;call&nbsp;my&nbsp;mobile&nbsp;phone&nbsp;number.

&gt;

&gt;Can&nbsp;we&nbsp;unsubscribe&nbsp;this&nbsp;email&nbsp;address&nbsp;please?&nbsp;I've&nbsp;now&nbsp;had&nbsp;a&nbsp;slew&nbsp;of&nbsp;

&gt;bounces&nbsp;from&nbsp;them.

&gt;

&gt;Thanks,

&gt;

&gt;Mark

&gt;

&gt;

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

&gt;

&gt;Message:&nbsp;3

&gt;Date:&nbsp;Mon,&nbsp;3&nbsp;Jan&nbsp;2011&nbsp;17:20:23&nbsp;-0800

&gt;From:&nbsp;Ramachandran&nbsp;G&nbsp;&lt;gtrama@gmail.com&gt;

&gt;Subject:&nbsp;[gmx-users]&nbsp;g_mindist

&gt;To:&nbsp;gmx-users@gromacs.org

&gt;Message-ID:

&gt;        &lt;AANLkTiktntrig9cT1zpQ3uFUPfOiY2pfAEbTA8B+thb4@mail.gmail.com&gt;

&gt;Content-Type:&nbsp;text/plain;&nbsp;charset="iso-8859-1"

&gt;

&gt;Hi&nbsp;Gromacs&nbsp;users,

&gt;&nbsp;&nbsp;&nbsp;&nbsp;I&nbsp;used&nbsp;g_mindist&nbsp;to&nbsp;calculate&nbsp;the&nbsp;minimum&nbsp;distance&nbsp;between&nbsp;a&nbsp;residue&nbsp;and

&gt;a&nbsp;group&nbsp;of&nbsp;water&nbsp;molecules.

&gt;Since&nbsp;distance&nbsp;is&nbsp;a&nbsp;length&nbsp;between&nbsp;two&nbsp;points&nbsp;in&nbsp;space,&nbsp;for&nbsp;the&nbsp;program

&gt;considers&nbsp;the&nbsp;bunch&nbsp;of&nbsp;water&nbsp;molecules(15&nbsp;number)

&gt;what&nbsp;specific&nbsp;point&nbsp;does&nbsp;the&nbsp;group&nbsp;consider&nbsp;?&nbsp;Thank&nbsp;you.

&gt;

&gt;Yours&nbsp;sincerely,

&gt;Rama

&gt;--------------&nbsp;next&nbsp;part&nbsp;--------------

&gt;An&nbsp;HTML&nbsp;attachment&nbsp;was&nbsp;scrubbed...

&gt;URL:&nbsp;http://lists.gromacs.org/pipermail/gmx-users/attachments/20110103/2a4eb0bf/attachment-0001.html

&gt;

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

&gt;

&gt;Message:&nbsp;4

&gt;Date:&nbsp;Mon,&nbsp;03&nbsp;Jan&nbsp;2011&nbsp;20:29:02&nbsp;-0500

&gt;From:&nbsp;"Justin&nbsp;A.&nbsp;Lemkul"&nbsp;&lt;jalemkul@vt.edu&gt;

&gt;Subject:&nbsp;Re:&nbsp;[gmx-users]&nbsp;g_mindist

&gt;To:&nbsp;Discussion&nbsp;list&nbsp;for&nbsp;GROMACS&nbsp;users&nbsp;&lt;gmx-users@gromacs.org&gt;

&gt;Message-ID:&nbsp;&lt;4D2277DE.6080008@vt.edu&gt;

&gt;Content-Type:&nbsp;text/plain;&nbsp;charset=ISO-8859-1;&nbsp;format=flowed

&gt;

&gt;

&gt;

&gt;Ramachandran&nbsp;G&nbsp;wrote:

&gt;&gt;&nbsp;Hi&nbsp;Gromacs&nbsp;users,

&gt;&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;I&nbsp;used&nbsp;g_mindist&nbsp;to&nbsp;calculate&nbsp;the&nbsp;minimum&nbsp;distance&nbsp;between&nbsp;a&nbsp;residue&nbsp;

&gt;&gt;&nbsp;and&nbsp;a&nbsp;group&nbsp;of&nbsp;water&nbsp;molecules.

&gt;&gt;&nbsp;Since&nbsp;distance&nbsp;is&nbsp;a&nbsp;length&nbsp;between&nbsp;two&nbsp;points&nbsp;in&nbsp;space,&nbsp;for&nbsp;the&nbsp;program&nbsp;

&gt;&gt;&nbsp;considers&nbsp;the&nbsp;bunch&nbsp;of&nbsp;water&nbsp;molecules(15&nbsp;number)

&gt;&gt;&nbsp;what&nbsp;specific&nbsp;point&nbsp;does&nbsp;the&nbsp;group&nbsp;consider&nbsp;?&nbsp;Thank&nbsp;you.

&gt;&gt;&nbsp;

&gt;

&gt;The&nbsp;distance&nbsp;measured&nbsp;is&nbsp;that&nbsp;between&nbsp;the&nbsp;two&nbsp;closest&nbsp;atoms,&nbsp;whichever&nbsp;those&nbsp;may&nbsp;

&gt;be.&nbsp;&nbsp;Read&nbsp;the&nbsp;first&nbsp;few&nbsp;sentences&nbsp;of&nbsp;g_mindist&nbsp;-h.

&gt;

&gt;-Justin

&gt;

&gt;&gt;&nbsp;Yours&nbsp;sincerely,

&gt;&gt;&nbsp;Rama

&gt;&gt;&nbsp;

&gt;&gt;&nbsp;

&gt;&gt;&nbsp;

&gt;

&gt;--&nbsp;

&gt;========================================

&gt;

&gt;Justin&nbsp;A.&nbsp;Lemkul

&gt;Ph.D.&nbsp;Candidate

&gt;ICTAS&nbsp;Doctoral&nbsp;Scholar

&gt;MILES-IGERT&nbsp;Trainee

&gt;Department&nbsp;of&nbsp;Biochemistry

&gt;Virginia&nbsp;Tech

&gt;Blacksburg,&nbsp;VA

&gt;jalemkul[at]vt.edu&nbsp;|&nbsp;(540)&nbsp;231-9080

&gt;http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

&gt;

&gt;========================================

&gt;

&gt;

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

&gt;

&gt;Message:&nbsp;5

&gt;Date:&nbsp;Tue,&nbsp;4&nbsp;Jan&nbsp;2011&nbsp;11:59:53&nbsp;+0530

&gt;From:&nbsp;sreelakshmi&nbsp;ramesh&nbsp;&lt;sree.lakshmi@research.iiit.ac.in&gt;

&gt;Subject:&nbsp;Re:&nbsp;[gmx-users]&nbsp;The&nbsp;sum&nbsp;of&nbsp;the&nbsp;O-H&nbsp;distancesof&nbsp;the&nbsp;backbone

&gt;        hydrogen        bonds&nbsp;ROH

&gt;To:&nbsp;Discussion&nbsp;list&nbsp;for&nbsp;GROMACS&nbsp;users&nbsp;&lt;gmx-users@gromacs.org&gt;

&gt;Message-ID:

&gt;        &lt;AANLkTikw-M-NCBpnkAj8RxnrVjrDEzYPsNCfmMbiHV0V@mail.gmail.com&gt;

&gt;Content-Type:&nbsp;text/plain;&nbsp;charset="iso-8859-1"

&gt;

&gt;Thanks&nbsp;a&nbsp;lot&nbsp;for&nbsp;your&nbsp;reply..

&gt;

&gt;On&nbsp;Mon,&nbsp;Jan&nbsp;3,&nbsp;2011&nbsp;at&nbsp;6:07&nbsp;PM,&nbsp;Mark&nbsp;Abraham&nbsp;&lt;Mark.Abraham@anu.edu.au&gt;wrote:

&gt;

&gt;&gt;&nbsp;On&nbsp;2/01/2011&nbsp;2:18&nbsp;PM,&nbsp;sreelakshmi&nbsp;ramesh&nbsp;wrote:

&gt;&gt;

&gt;&gt;&gt;&nbsp;Dear&nbsp;all,

&gt;&gt;&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;I&nbsp;have&nbsp;a&nbsp;protein&nbsp;in&nbsp;water&nbsp;and&nbsp;i&nbsp;have&nbsp;simulated&nbsp;it&nbsp;for&nbsp;few

&gt;&gt;&gt;&nbsp;nanoseconds&nbsp;and&nbsp;i&nbsp;now&nbsp;i&nbsp;wanted&nbsp;to&nbsp;monitor&nbsp;the&nbsp;&nbsp;The&nbsp;sum&nbsp;of&nbsp;the&nbsp;O-H&nbsp;distances

&gt;&gt;&gt;&nbsp;(in&nbsp;Å)&nbsp;of&nbsp;the&nbsp;backbone

&gt;&gt;&gt;&nbsp;hydrogen&nbsp;bonds&nbsp;ROH:i&nbsp;dono&nbsp;how&nbsp;to&nbsp;extract&nbsp;the&nbsp;value&nbsp;from&nbsp;the&nbsp;trajectory

&gt;&gt;&gt;&nbsp;file.Any&nbsp;siuggestion&nbsp;please.Thanks&nbsp;in&nbsp;advance

&gt;&gt;&gt;

&gt;&gt;

&gt;&gt;&nbsp;Look&nbsp;in&nbsp;section&nbsp;7.4&nbsp;of&nbsp;the&nbsp;manual&nbsp;for&nbsp;a&nbsp;suitable&nbsp;tool&nbsp;for&nbsp;extracting&nbsp;the

&gt;&gt;&nbsp;raw&nbsp;distances.&nbsp;You'll&nbsp;need&nbsp;some&nbsp;other&nbsp;non-GROMACS&nbsp;tool&nbsp;to&nbsp;add&nbsp;them&nbsp;up.

&gt;&gt;

&gt;&gt;&nbsp;Mark

&gt;&gt;&nbsp;--

&gt;&gt;&nbsp;gmx-users&nbsp;mailing&nbsp;list&nbsp;&nbsp;&nbsp;&nbsp;gmx-users@gromacs.org

&gt;&gt;&nbsp;http://lists.gromacs.org/mailman/listinfo/gmx-users

&gt;&gt;&nbsp;Please&nbsp;search&nbsp;the&nbsp;archive&nbsp;at

&gt;&gt;&nbsp;http://www.gromacs.org/Support/Mailing_Lists/Search&nbsp;before&nbsp;posting!

&gt;&gt;&nbsp;Please&nbsp;don't&nbsp;post&nbsp;(un)subscribe&nbsp;requests&nbsp;to&nbsp;the&nbsp;list.&nbsp;Use&nbsp;the&nbsp;www&nbsp;interface

&gt;&gt;&nbsp;or&nbsp;send&nbsp;it&nbsp;to&nbsp;gmx-users-request@gromacs.org.

&gt;&gt;&nbsp;Can't&nbsp;post?&nbsp;Read&nbsp;http://www.gromacs.org/Support/Mailing_Lists

&gt;&gt;

&gt;--------------&nbsp;next&nbsp;part&nbsp;--------------

&gt;An&nbsp;HTML&nbsp;attachment&nbsp;was&nbsp;scrubbed...

&gt;URL:&nbsp;http://lists.gromacs.org/pipermail/gmx-users/attachments/20110104/fd6404ca/attachment-0001.html

&gt;

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

&gt;

&gt;Message:&nbsp;6

&gt;Date:&nbsp;Tue,&nbsp;4&nbsp;Jan&nbsp;2011&nbsp;15:45:57&nbsp;+0800&nbsp;(CST)

&gt;From:&nbsp;gromacs&nbsp;&lt;ptf1242@163.com&gt;

&gt;Subject:&nbsp;[gmx-users]&nbsp;How&nbsp;to&nbsp;get&nbsp;sufactant.gro,&nbsp;sufactant.top,

&gt;To:&nbsp;gmx-users@gromacs.org

&gt;Message-ID:&nbsp;&lt;7bda4963.110c4.12d4ffd516f.Coremail.ptf1242@163.com&gt;

&gt;Content-Type:&nbsp;text/plain;&nbsp;charset="gbk"

&gt;

&gt;Hi&nbsp;expert,

&gt;&nbsp;

&gt;I'd&nbsp;like&nbsp;to&nbsp;add&nbsp;sufactant&nbsp;to&nbsp;water.&nbsp;That&nbsp;means&nbsp;i&nbsp;should&nbsp;first&nbsp;get&nbsp;the&nbsp;sufactant.gro,&nbsp;and&nbsp;sufactant.top.

&gt;&nbsp;

&gt;Someone&nbsp;said&nbsp;that&nbsp;we&nbsp;cannot&nbsp;get&nbsp;sufactant.gro&nbsp;and&nbsp;sufactant.top&nbsp;through&nbsp;grompp&nbsp;()&nbsp;&nbsp;sufactant.pdb.&nbsp;Because&nbsp;grompp&nbsp;&nbsp;.pdb&nbsp;could&nbsp;mainly&nbsp;use&nbsp;for&nbsp;macro-biology&nbsp;big&nbsp;moleculars,&nbsp;which&nbsp;means&nbsp;some&nbsp;proteins&nbsp;etc.

&gt;So&nbsp;that&nbsp;means&nbsp;we&nbsp;could&nbsp;not&nbsp;get&nbsp;correct&nbsp;&nbsp;.gro,&nbsp;.top&nbsp;small&nbsp;molecules&nbsp;such&nbsp;as&nbsp;inorganic&nbsp;or&nbsp;small&nbsp;organic&nbsp;molecules&nbsp;(such&nbsp;asethanol).

&gt;&nbsp;

&gt;So&nbsp;how&nbsp;can&nbsp;we&nbsp;get&nbsp;the&nbsp;sufactant.gro,&nbsp;sufactant.top?&nbsp;and&nbsp;which&nbsp;force&nbsp;field&nbsp;should&nbsp;we&nbsp;choose&nbsp;for&nbsp;ordinary&nbsp;simulation?&nbsp;I&nbsp;know&nbsp;we&nbsp;often&nbsp;use&nbsp;ffoplass&nbsp;force&nbsp;field&nbsp;for&nbsp;solution.

&gt;&nbsp;

&gt;Tiefeng

&gt;--------------&nbsp;next&nbsp;part&nbsp;--------------

&gt;An&nbsp;HTML&nbsp;attachment&nbsp;was&nbsp;scrubbed...

&gt;URL:&nbsp;http://lists.gromacs.org/pipermail/gmx-users/attachments/20110104/7ebcc6f6/attachment-0001.html

&gt;

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

&gt;

&gt;Message:&nbsp;7

&gt;Date:&nbsp;Tue,&nbsp;04&nbsp;Jan&nbsp;2011&nbsp;19:18:10&nbsp;+1100

&gt;From:&nbsp;Mark&nbsp;Abraham&nbsp;&lt;mark.abraham@anu.edu.au&gt;

&gt;Subject:&nbsp;Re:&nbsp;[gmx-users]&nbsp;How&nbsp;to&nbsp;get&nbsp;sufactant.gro,&nbsp;sufactant.top,

&gt;To:&nbsp;Discussion&nbsp;list&nbsp;for&nbsp;GROMACS&nbsp;users&nbsp;&lt;gmx-users@gromacs.org&gt;

&gt;Message-ID:&nbsp;&lt;7690a1161265.4d237272@anu.edu.au&gt;

&gt;Content-Type:&nbsp;text/plain;&nbsp;charset="iso-8859-1"

&gt;

&gt;On&nbsp;01/04/11,&nbsp;gromacs&nbsp;&nbsp;&lt;ptf1242@163.com&gt;&nbsp;wrote:

&gt;&gt;&nbsp;Hi&nbsp;expert,

&gt;&gt;&nbsp;

&gt;&gt;&nbsp;&nbsp;

&gt;&gt;&nbsp;

&gt;&gt;&nbsp;I'd&nbsp;like&nbsp;to&nbsp;add&nbsp;sufactant&nbsp;to&nbsp;water.&nbsp;That&nbsp;means&nbsp;i&nbsp;should&nbsp;first&nbsp;get&nbsp;the&nbsp;sufactant.gro,&nbsp;and&nbsp;sufactant.top.

&gt;&gt;&nbsp;

&gt;&gt;&nbsp;

&gt;

&gt;No,&nbsp;you&nbsp;need&nbsp;a&nbsp;coordinate&nbsp;file&nbsp;for&nbsp;the&nbsp;starting&nbsp;point&nbsp;for&nbsp;your&nbsp;GROMACS&nbsp;work,&nbsp;and&nbsp;the&nbsp;pieces&nbsp;to&nbsp;combine&nbsp;into&nbsp;a&nbsp;.top.&nbsp;That&nbsp;might&nbsp;mean&nbsp;a&nbsp;coordinate&nbsp;file&nbsp;of&nbsp;all&nbsp;your&nbsp;surfactant&nbsp;molecules&nbsp;and&nbsp;matching&nbsp;.top&nbsp;file&nbsp;that&nbsp;you&nbsp;then&nbsp;solvate&nbsp;with&nbsp;genbox.&nbsp;Or&nbsp;you&nbsp;might&nbsp;want&nbsp;to&nbsp;use&nbsp;genconf&nbsp;to&nbsp;replicate&nbsp;some&nbsp;existing&nbsp;coordinate&nbsp;file&nbsp;somehow.&nbsp;Or&nbsp;you&nbsp;might&nbsp;have&nbsp;your&nbsp;starting&nbsp;point&nbsp;already&nbsp;and&nbsp;need&nbsp;to&nbsp;match&nbsp;a&nbsp;.top&nbsp;to&nbsp;it.

&gt;&nbsp;

&gt;

&gt;&gt;&nbsp;

&gt;&gt;&nbsp;Someone&nbsp;said&nbsp;that&nbsp;we&nbsp;cannot&nbsp;get&nbsp;sufactant.gro&nbsp;and&nbsp;sufactant.top&nbsp;through&nbsp;grompp&nbsp;()&nbsp;&nbsp;sufactant.pdb.&nbsp;Because&nbsp;grompp&nbsp;&nbsp;.pdb&nbsp;could&nbsp;mainly&nbsp;use&nbsp;for&nbsp;macro-biology&nbsp;big&nbsp;moleculars,&nbsp;which&nbsp;means&nbsp;some&nbsp;proteins&nbsp;etc.

&gt;&gt;&nbsp;

&gt;&gt;&nbsp;

&gt;

&gt;Well&nbsp;they&nbsp;(or&nbsp;your&nbsp;account&nbsp;of&nbsp;them)&nbsp;is&nbsp;wrong&nbsp;on&nbsp;what&nbsp;might&nbsp;be&nbsp;several&nbsp;points.&nbsp;Someone&nbsp;needs&nbsp;to&nbsp;understand&nbsp;GROMACS&nbsp;workflows&nbsp;better&nbsp;-&nbsp;perhaps&nbsp;by&nbsp;doing&nbsp;some&nbsp;tutorial&nbsp;material&nbsp;and/or&nbsp;reading&nbsp;http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation

&gt;

&gt;

&gt;&gt;&nbsp;

&gt;&gt;&nbsp;

&gt;&gt;&nbsp;So&nbsp;that&nbsp;means&nbsp;we&nbsp;could&nbsp;not&nbsp;get&nbsp;correct&nbsp;&nbsp;.gro,&nbsp;.top&nbsp;small&nbsp;molecules&nbsp;such&nbsp;as&nbsp;inorganic&nbsp;or&nbsp;small&nbsp;organic&nbsp;molecules&nbsp;(such&nbsp;as&nbsp;ethanol).

&gt;&gt;&nbsp;

&gt;&gt;&nbsp;&nbsp;

&gt;&gt;&nbsp;

&gt;&gt;&nbsp;So&nbsp;how&nbsp;can&nbsp;we&nbsp;get&nbsp;the&nbsp;sufactant.gro,&nbsp;sufactant.top?

&gt;&gt;&nbsp;

&gt;&gt;&nbsp;

&gt;

&gt;That&nbsp;varies&nbsp;widely&nbsp;with&nbsp;what&nbsp;raw&nbsp;materials&nbsp;exist&nbsp;and&nbsp;what&nbsp;the&nbsp;objective&nbsp;is.

&gt;

&gt;

&gt;&gt;&nbsp;&nbsp;and&nbsp;which&nbsp;force&nbsp;field&nbsp;should&nbsp;we&nbsp;choose&nbsp;for&nbsp;ordinary&nbsp;simulation?&nbsp;I&nbsp;know&nbsp;we&nbsp;often&nbsp;use&nbsp;ffoplass&nbsp;force&nbsp;field&nbsp;for&nbsp;solution.

&gt;&gt;&nbsp;

&gt;&gt;&nbsp;

&gt;

&gt;That's&nbsp;your&nbsp;homework,&nbsp;I'm&nbsp;afraid.&nbsp;See&nbsp;above&nbsp;link.

&gt;

&gt;Mark

&gt;

&gt;

&gt;--------------&nbsp;next&nbsp;part&nbsp;--------------

&gt;An&nbsp;HTML&nbsp;attachment&nbsp;was&nbsp;scrubbed...

&gt;URL:&nbsp;http://lists.gromacs.org/pipermail/gmx-users/attachments/20110104/2ea4f216/attachment.html

&gt;

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

&gt;

&gt;--&nbsp;

&gt;gmx-users&nbsp;mailing&nbsp;list

&gt;gmx-users@gromacs.org

&gt;http://lists.gromacs.org/mailman/listinfo/gmx-users

&gt;Please&nbsp;search&nbsp;the&nbsp;archive&nbsp;at&nbsp;http://www.gromacs.org/Support/Mailing_Lists/Search&nbsp;before&nbsp;posting!

&gt;

&gt;End&nbsp;of&nbsp;gmx-users&nbsp;Digest,&nbsp;Vol&nbsp;81,&nbsp;Issue&nbsp;15

&gt;*****************************************

</PRE><br><br><span title="neteasefooter"><span id="netease_mail_footer"></span></span>