<DIV>Dear Prof. Justin A. Lemkul,</DIV>

<DIV>&nbsp;</DIV>

<DIV>Thanks very much for the website you supplied. It is very useful to me! Thank you again!<BR></DIV>

<DIV>--<BR>

<P align="left"><U>Best wishes,</U></P>

<P align="left"><U>Qinghua Liao</U></P>

<P align="left"><U>Ph.D student of Tianjin University, China</U></P></DIV><BR><PRE><BR>At&nbsp;2011-04-10，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;NPT.mdp&nbsp;parameters&nbsp;NOTE&nbsp;(Peter&nbsp;C.&nbsp;Lai)

&gt;&nbsp;&nbsp;&nbsp;2.&nbsp;Re:&nbsp;converging&nbsp;value&nbsp;(Mark&nbsp;Abraham)

&gt;&nbsp;&nbsp;&nbsp;3.&nbsp;Re:&nbsp;Dangling&nbsp;bond&nbsp;error&nbsp;for&nbsp;dna&nbsp;(Justin&nbsp;A.&nbsp;Lemkul)

&gt;&nbsp;&nbsp;&nbsp;4.&nbsp;probelm&nbsp;of&nbsp;using&nbsp;amber&nbsp;force&nbsp;field&nbsp;(fancy2012)

&gt;&nbsp;&nbsp;&nbsp;5.&nbsp;Re:&nbsp;probelm&nbsp;of&nbsp;using&nbsp;amber&nbsp;force&nbsp;field&nbsp;(Justin&nbsp;A.&nbsp;Lemkul)

&gt;&nbsp;&nbsp;&nbsp;6.&nbsp;Re:&nbsp;converging&nbsp;value&nbsp;(mohsen&nbsp;ramezanpour)

&gt;&nbsp;&nbsp;&nbsp;7.&nbsp;Re:&nbsp;converging&nbsp;value&nbsp;(Mark&nbsp;Abraham)

&gt;

&gt;

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

&gt;

&gt;Message:&nbsp;1

&gt;Date:&nbsp;Sun,&nbsp;10&nbsp;Apr&nbsp;2011&nbsp;05:02:10&nbsp;-0500

&gt;From:&nbsp;"Peter&nbsp;C.&nbsp;Lai"&nbsp;&lt;pcl@uab.edu&gt;

&gt;Subject:&nbsp;Re:&nbsp;[gmx-users]&nbsp;NPT.mdp&nbsp;parameters&nbsp;NOTE

&gt;To:&nbsp;mohsen&nbsp;ramezanpour&nbsp;&lt;ramezanpour.mohsen@gmail.com&gt;

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

&gt;Message-ID:&nbsp;&lt;20110410100210.GI54289@cesium.hyperfine.info&gt;

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

&gt;

&gt;He&nbsp;told&nbsp;me&nbsp;you&nbsp;can&nbsp;use&nbsp;up&nbsp;to&nbsp;0.5&nbsp;in&nbsp;an&nbsp;off-list&nbsp;email&nbsp;and&nbsp;in&nbsp;fact,&nbsp;does&nbsp;so

&gt;in&nbsp;the&nbsp;KALP-15&nbsp;in&nbsp;DPPC&nbsp;example...

&gt;

&gt;On&nbsp;2011-04-10&nbsp;02:54:15AM&nbsp;-0500,&nbsp;mohsen&nbsp;ramezanpour&nbsp;wrote:

&gt;&gt;&nbsp;Dear&nbsp;Dr.Justin

&gt;&gt;&nbsp;

&gt;&gt;&nbsp;As&nbsp;you&nbsp;have&nbsp;noticed&nbsp;in&nbsp;your&nbsp;tutorials,It&nbsp;is&nbsp;better&nbsp;to&nbsp;use&nbsp;Nose-Hoover&nbsp;for&nbsp;tempreture&nbsp;in&nbsp;the&nbsp;NPT.mdp&nbsp;file.

&gt;&gt;&nbsp;You&nbsp;have&nbsp;used&nbsp;tau-t&nbsp;=&nbsp;0.1&nbsp;in&nbsp;most&nbsp;of&nbsp;your&nbsp;md.mdp&nbsp;files&nbsp;for&nbsp;generating&nbsp;npt&nbsp;ensemble.

&gt;&gt;&nbsp;

&gt;&gt;&nbsp;When&nbsp;I&nbsp;use&nbsp;a&nbsp;npt&nbsp;file&nbsp;with&nbsp;these&nbsp;settings,there&nbsp;is&nbsp;a&nbsp;Note&nbsp;as&nbsp;following:

&gt;&gt;&nbsp;sorry,i&nbsp;can't&nbsp;remember&nbsp;the&nbsp;exact&nbsp;messge&nbsp;but&nbsp;:it&nbsp;says&nbsp;it&nbsp;is&nbsp;better&nbsp;to&nbsp;use&nbsp;a&nbsp;tau_t&nbsp;&nbsp;&nbsp;20&nbsp;times&nbsp;of&nbsp;another&nbsp;quantity,

&gt;&gt;&nbsp;in&nbsp;my&nbsp;work&nbsp;the&nbsp;quantity=0.01

&gt;&gt;&nbsp;

&gt;&gt;&nbsp;When&nbsp;I&nbsp;made&nbsp;tau_t=0.2&nbsp;there&nbsp;was&nbsp;not&nbsp;any&nbsp;Note!

&gt;&gt;&nbsp;

&gt;&gt;&nbsp;Can&nbsp;I&nbsp;ignore&nbsp;this&nbsp;Note?Is&nbsp;it&nbsp;safe&nbsp;continuing&nbsp;with&nbsp;the&nbsp;same&nbsp;tau_t=0.1&nbsp;as&nbsp;you&nbsp;used?

&gt;&gt;&nbsp;

&gt;

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

&gt;&gt;&nbsp;www&nbsp;interface&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;

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

&gt;Peter&nbsp;C.&nbsp;Lai&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;|&nbsp;University&nbsp;of&nbsp;Alabama-Birmingham

&gt;Programmer/Analyst&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;|&nbsp;BEC&nbsp;257

&gt;Genetics,&nbsp;Div.&nbsp;of&nbsp;Research&nbsp;&nbsp;&nbsp;|&nbsp;1150&nbsp;10th&nbsp;Avenue&nbsp;South

&gt;pcl@uab.edu&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;|&nbsp;Birmingham&nbsp;AL&nbsp;35294-4461

&gt;(205)&nbsp;690-0808&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;|

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

&gt;

&gt;

&gt;

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

&gt;

&gt;Message:&nbsp;2

&gt;Date:&nbsp;Sun,&nbsp;10&nbsp;Apr&nbsp;2011&nbsp;20:39:25&nbsp;+1000

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

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

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

&gt;Message-ID:&nbsp;&lt;4DA188DD.7090804@anu.edu.au&gt;

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

&gt;

&gt;On&nbsp;10/04/2011&nbsp;6:48&nbsp;PM,&nbsp;mohsen&nbsp;ramezanpour&nbsp;wrote:

&gt;&gt;&nbsp;Dear&nbsp;All

&gt;&gt;

&gt;&gt;&nbsp;How&nbsp;can&nbsp;I&nbsp;determine&nbsp;the&nbsp;converged&nbsp;value&nbsp;of&nbsp;a&nbsp;simulation?

&gt;&gt;&nbsp;Because&nbsp;the&nbsp;pressure&nbsp;has&nbsp;big&nbsp;oscilations&nbsp;around&nbsp;it's&nbsp;converging&nbsp;value&nbsp;

&gt;&gt;&nbsp;but&nbsp;it&nbsp;is&nbsp;difficult&nbsp;to&nbsp;determine&nbsp;that&nbsp;value.

&gt;

&gt;Longer&nbsp;simulations&nbsp;on&nbsp;bigger&nbsp;systems.

&gt;

&gt;Mark

&gt;

&gt;

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

&gt;

&gt;Message:&nbsp;3

&gt;Date:&nbsp;Sun,&nbsp;10&nbsp;Apr&nbsp;2011&nbsp;07:17:59&nbsp;-0400

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

&gt;Subject:&nbsp;Re:&nbsp;[gmx-users]&nbsp;Dangling&nbsp;bond&nbsp;error&nbsp;for&nbsp;dna

&gt;To:&nbsp;"Gromacs&nbsp;Users'&nbsp;List"&nbsp;&lt;gmx-users@gromacs.org&gt;

&gt;Message-ID:&nbsp;&lt;4DA191E7.3030707@vt.edu&gt;

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

&gt;

&gt;

&gt;

&gt;majid&nbsp;hasan&nbsp;wrote:

&gt;&gt;&nbsp;Sorry,&nbsp;the&nbsp;pdb&nbsp;file&nbsp;is&nbsp;bigger&nbsp;than&nbsp;50k&nbsp;so&nbsp;it&nbsp;won't&nbsp;attach,&nbsp;so&nbsp;its&nbsp;pasted&nbsp;

&gt;&gt;&nbsp;below.&nbsp;Output&nbsp;of&nbsp;pdb2gmx&nbsp;is&nbsp;attached.

&gt;&gt;&nbsp;

&gt;

&gt;You&nbsp;have&nbsp;numerous&nbsp;problems&nbsp;with&nbsp;this&nbsp;.pdb&nbsp;file:

&gt;

&gt;1.&nbsp;All&nbsp;residues&nbsp;are&nbsp;listed&nbsp;as&nbsp;being&nbsp;the&nbsp;3'&nbsp;end&nbsp;form.&nbsp;&nbsp;Your&nbsp;chain&nbsp;should&nbsp;start&nbsp;

&gt;with&nbsp;a&nbsp;5'&nbsp;end,&nbsp;include&nbsp;the&nbsp;"middle"&nbsp;residues,&nbsp;and&nbsp;end&nbsp;with&nbsp;a&nbsp;3'&nbsp;form.

&gt;

&gt;2.&nbsp;5'&nbsp;ends&nbsp;do&nbsp;not&nbsp;have&nbsp;phosphate&nbsp;on&nbsp;them,&nbsp;per&nbsp;force&nbsp;field&nbsp;convention.

&gt;

&gt;3.&nbsp;You&nbsp;have&nbsp;various&nbsp;incorrect&nbsp;atoms,&nbsp;and&nbsp;some&nbsp;incorrect&nbsp;atom&nbsp;names.

&gt;

&gt;Please&nbsp;refer&nbsp;to&nbsp;the&nbsp;dna.rtp&nbsp;file&nbsp;for&nbsp;your&nbsp;chosen&nbsp;force&nbsp;field&nbsp;to&nbsp;understand&nbsp;its&nbsp;

&gt;expectations.&nbsp;&nbsp;Then&nbsp;you&nbsp;will&nbsp;need&nbsp;to&nbsp;manually&nbsp;fix&nbsp;your&nbsp;.pdb&nbsp;file&nbsp;by&nbsp;renaming,&nbsp;

&gt;replacing,&nbsp;or&nbsp;removing&nbsp;whatever&nbsp;is&nbsp;in&nbsp;conflict.

&gt;

&gt;-Justin

&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;4

&gt;Date:&nbsp;Sun,&nbsp;10&nbsp;Apr&nbsp;2011&nbsp;18:55:15&nbsp;+0800&nbsp;(CST)

&gt;From:&nbsp;fancy2012&nbsp;&lt;fancy2012@yeah.net&gt;

&gt;Subject:&nbsp;[gmx-users]&nbsp;probelm&nbsp;of&nbsp;using&nbsp;amber&nbsp;force&nbsp;field

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

&gt;Message-ID:&nbsp;&lt;3ec402b.63dd.12f3f0d1e61.Coremail.fancy2012@yeah.net&gt;

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

&gt;

&gt;Dear&nbsp;GMX&nbsp;users,

&gt;&nbsp;

&gt;I&nbsp;have&nbsp;a&nbsp;question&nbsp;about&nbsp;running&nbsp;MD&nbsp;simulation&nbsp;using&nbsp;amber&nbsp;force&nbsp;field.&nbsp;It&nbsp;is&nbsp;easy&nbsp;to&nbsp;prepare&nbsp;the&nbsp;top&nbsp;and&nbsp;gro&nbsp;files&nbsp;of&nbsp;protein&nbsp;with&nbsp;amber&nbsp;force&nbsp;field,&nbsp;but&nbsp;how&nbsp;should&nbsp;I&nbsp;prepare&nbsp;the&nbsp;itp&nbsp;and&nbsp;gro&nbsp;files&nbsp;of&nbsp;small&nbsp;molecules&nbsp;&nbsp;with&nbsp;GAFF&nbsp;force&nbsp;field?&nbsp;I&nbsp;know&nbsp;the&nbsp;program&nbsp;ANTECHAMBER&nbsp;and&nbsp;tleap&nbsp;can&nbsp;generate&nbsp;the&nbsp;some&nbsp;molecule's&nbsp;topology&nbsp;and&nbsp;coordinate.&nbsp;Could&nbsp;someone&nbsp;give&nbsp;me&nbsp;some&nbsp;hints?&nbsp;Thanks&nbsp;very&nbsp;much&nbsp;in&nbsp;advance!

&gt;&nbsp;

&gt;--

&gt;

&gt;

&gt;Best&nbsp;wishes,

&gt;

&gt;Qinghua&nbsp;Liao

&gt;

&gt;Ph.D&nbsp;student&nbsp;of&nbsp;Tianjin&nbsp;University,&nbsp;China

&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/20110410/b7b8202b/attachment-0001.html

&gt;

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

&gt;

&gt;Message:&nbsp;5

&gt;Date:&nbsp;Sun,&nbsp;10&nbsp;Apr&nbsp;2011&nbsp;07:32:13&nbsp;-0400

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

&gt;Subject:&nbsp;Re:&nbsp;[gmx-users]&nbsp;probelm&nbsp;of&nbsp;using&nbsp;amber&nbsp;force&nbsp;field

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

&gt;Message-ID:&nbsp;&lt;4DA1953D.7060006@vt.edu&gt;

&gt;Content-Type:&nbsp;text/plain;&nbsp;charset=x-gbk;&nbsp;format=flowed

&gt;

&gt;

&gt;

&gt;fancy2012&nbsp;wrote:

&gt;&gt;&nbsp;Dear&nbsp;GMX&nbsp;users,

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

&gt;&gt;&nbsp;I&nbsp;have&nbsp;a&nbsp;question&nbsp;about&nbsp;running&nbsp;MD&nbsp;simulation&nbsp;using&nbsp;amber&nbsp;force&nbsp;

&gt;&gt;&nbsp;field.&nbsp;It&nbsp;is&nbsp;easy&nbsp;to&nbsp;prepare&nbsp;the&nbsp;top&nbsp;and&nbsp;gro&nbsp;files&nbsp;of&nbsp;protein&nbsp;with&nbsp;amber&nbsp;

&gt;&gt;&nbsp;force&nbsp;field,&nbsp;but&nbsp;how&nbsp;should&nbsp;I&nbsp;prepare&nbsp;the&nbsp;itp&nbsp;and&nbsp;gro&nbsp;files&nbsp;of&nbsp;small&nbsp;

&gt;&gt;&nbsp;molecules&nbsp;&nbsp;with&nbsp;GAFF&nbsp;force&nbsp;field?&nbsp;I&nbsp;know&nbsp;the&nbsp;program&nbsp;ANTECHAMBER&nbsp;and&nbsp;

&gt;&gt;&nbsp;tleap&nbsp;can&nbsp;generate&nbsp;the&nbsp;some&nbsp;molecule's&nbsp;topology&nbsp;and&nbsp;coordinate.&nbsp;Could&nbsp;

&gt;&gt;&nbsp;someone&nbsp;give&nbsp;me&nbsp;some&nbsp;hints?&nbsp;Thanks&nbsp;very&nbsp;much&nbsp;in&nbsp;advance!

&gt;

&gt;http://code.google.com/p/acpype/&nbsp;is&nbsp;one&nbsp;common&nbsp;approach.

&gt;

&gt;-Justin

&gt;

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

&gt;&gt;&nbsp;--

&gt;&gt;&nbsp;

&gt;&gt;&nbsp;_Best&nbsp;wishes,_

&gt;&gt;&nbsp;

&gt;&gt;&nbsp;_Qinghua&nbsp;Liao_

&gt;&gt;&nbsp;

&gt;&gt;&nbsp;_Ph.D&nbsp;student&nbsp;of&nbsp;Tianjin&nbsp;University,&nbsp;China_

&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;6

&gt;Date:&nbsp;Sun,&nbsp;10&nbsp;Apr&nbsp;2011&nbsp;16:11:28&nbsp;+0430

&gt;From:&nbsp;mohsen&nbsp;ramezanpour&nbsp;&lt;ramezanpour.mohsen@gmail.com&gt;

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

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

&gt;Message-ID:&nbsp;&lt;BANLkTimNexPd1MujGF4b9zjAi4_RM_MpUw@mail.gmail.com&gt;

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

&gt;

&gt;Dear&nbsp;Dr.Mark

&gt;

&gt;thank&nbsp;you&nbsp;for&nbsp;your&nbsp;attention

&gt;How&nbsp;long&nbsp;is&nbsp;enough?

&gt;for&nbsp;example&nbsp;I&nbsp;have&nbsp;run&nbsp;200&nbsp;ps&nbsp;for&nbsp;making&nbsp;npt(p=1&nbsp;bar)&nbsp;for&nbsp;my&nbsp;system&nbsp;(300

&gt;nm^3)

&gt;But&nbsp;the&nbsp;pressure&nbsp;is&nbsp;oscilating&nbsp;so&nbsp;much,and&nbsp;I&nbsp;can't&nbsp;be&nbsp;sure&nbsp;if&nbsp;it&nbsp;has

&gt;converged&nbsp;or&nbsp;not!

&gt;of&nbsp;course&nbsp;its&nbsp;average&nbsp;is&nbsp;approximately&nbsp;5&nbsp;bar&nbsp;(at&nbsp;the&nbsp;end&nbsp;of&nbsp;log&nbsp;file)

&gt;

&gt;Do&nbsp;you&nbsp;have&nbsp;any&nbsp;idea?

&gt;I&nbsp;know&nbsp;it&nbsp;is&nbsp;not&nbsp;any&nbsp;problem&nbsp;if&nbsp;a&nbsp;quantity&nbsp;is&nbsp;oscilating&nbsp;around&nbsp;it's

&gt;converged&nbsp;value.

&gt;

&gt;thanks&nbsp;in&nbsp;advance&nbsp;for&nbsp;your&nbsp;reply

&gt;

&gt;On&nbsp;Sun,&nbsp;Apr&nbsp;10,&nbsp;2011&nbsp;at&nbsp;3:09&nbsp;PM,&nbsp;Mark&nbsp;Abraham&nbsp;&lt;Mark.Abraham@anu.edu.au&gt;wrote:

&gt;

&gt;&gt;&nbsp;On&nbsp;10/04/2011&nbsp;6:48&nbsp;PM,&nbsp;mohsen&nbsp;ramezanpour&nbsp;wrote:

&gt;&gt;

&gt;&gt;&gt;&nbsp;Dear&nbsp;All

&gt;&gt;&gt;

&gt;&gt;&gt;&nbsp;How&nbsp;can&nbsp;I&nbsp;determine&nbsp;the&nbsp;converged&nbsp;value&nbsp;of&nbsp;a&nbsp;simulation?

&gt;&gt;&gt;&nbsp;Because&nbsp;the&nbsp;pressure&nbsp;has&nbsp;big&nbsp;oscilations&nbsp;around&nbsp;it's&nbsp;converging&nbsp;value&nbsp;but

&gt;&gt;&gt;&nbsp;it&nbsp;is&nbsp;difficult&nbsp;to&nbsp;determine&nbsp;that&nbsp;value.

&gt;&gt;&gt;

&gt;&gt;

&gt;&gt;&nbsp;Longer&nbsp;simulations&nbsp;on&nbsp;bigger&nbsp;systems.

&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/20110410/d6cde97e/attachment-0001.html

&gt;

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

&gt;

&gt;Message:&nbsp;7

&gt;Date:&nbsp;Sun,&nbsp;10&nbsp;Apr&nbsp;2011&nbsp;21:57:12&nbsp;+1000

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

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

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

&gt;Message-ID:&nbsp;&lt;4DA19B18.2030501@anu.edu.au&gt;

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

&gt;

&gt;On&nbsp;10/04/2011&nbsp;9:41&nbsp;PM,&nbsp;mohsen&nbsp;ramezanpour&nbsp;wrote:

&gt;&gt;&nbsp;Dear&nbsp;Dr.Mark

&gt;&gt;

&gt;&gt;&nbsp;thank&nbsp;you&nbsp;for&nbsp;your&nbsp;attention

&gt;&gt;&nbsp;How&nbsp;long&nbsp;is&nbsp;enough?

&gt;

&gt;For&nbsp;example,&nbsp;when&nbsp;the&nbsp;size&nbsp;of&nbsp;error&nbsp;estimate&nbsp;reported&nbsp;by&nbsp;g_energy&nbsp;is&nbsp;

&gt;smaller&nbsp;than&nbsp;the&nbsp;quantity&nbsp;you&nbsp;are&nbsp;trying&nbsp;to&nbsp;observe.&nbsp;That&nbsp;might&nbsp;take&nbsp;

&gt;many&nbsp;nanoseconds&nbsp;in&nbsp;the&nbsp;case&nbsp;of&nbsp;observables&nbsp;based&nbsp;on&nbsp;fluctuations&nbsp;of&nbsp;

&gt;atomic&nbsp;positions.&nbsp;There've&nbsp;been&nbsp;lots&nbsp;of&nbsp;mailing&nbsp;list&nbsp;threads&nbsp;on&nbsp;this&nbsp;topic.

&gt;

&gt;Mark

&gt;

&gt;&gt;&nbsp;for&nbsp;example&nbsp;I&nbsp;have&nbsp;run&nbsp;200&nbsp;ps&nbsp;for&nbsp;making&nbsp;npt(p=1&nbsp;bar)&nbsp;for&nbsp;my&nbsp;system&nbsp;

&gt;&gt;&nbsp;(300&nbsp;nm^3)

&gt;&gt;&nbsp;But&nbsp;the&nbsp;pressure&nbsp;is&nbsp;oscilating&nbsp;so&nbsp;much,and&nbsp;I&nbsp;can't&nbsp;be&nbsp;sure&nbsp;if&nbsp;it&nbsp;has&nbsp;

&gt;&gt;&nbsp;converged&nbsp;or&nbsp;not!

&gt;&gt;&nbsp;of&nbsp;course&nbsp;its&nbsp;average&nbsp;is&nbsp;approximately&nbsp;5&nbsp;bar&nbsp;(at&nbsp;the&nbsp;end&nbsp;of&nbsp;log&nbsp;file)

&gt;&gt;

&gt;&gt;&nbsp;Do&nbsp;you&nbsp;have&nbsp;any&nbsp;idea?

&gt;&gt;&nbsp;I&nbsp;know&nbsp;it&nbsp;is&nbsp;not&nbsp;any&nbsp;problem&nbsp;if&nbsp;a&nbsp;quantity&nbsp;is&nbsp;oscilating&nbsp;around&nbsp;it's&nbsp;

&gt;&gt;&nbsp;converged&nbsp;value.

&gt;&gt;

&gt;&gt;&nbsp;thanks&nbsp;in&nbsp;advance&nbsp;for&nbsp;your&nbsp;reply

&gt;&gt;

&gt;&gt;&nbsp;On&nbsp;Sun,&nbsp;Apr&nbsp;10,&nbsp;2011&nbsp;at&nbsp;3:09&nbsp;PM,&nbsp;Mark&nbsp;Abraham&nbsp;&lt;Mark.Abraham@anu.edu.au&nbsp;

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

&gt;&gt;

&gt;&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;On&nbsp;10/04/2011&nbsp;6:48&nbsp;PM,&nbsp;mohsen&nbsp;ramezanpour&nbsp;wrote:

&gt;&gt;

&gt;&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Dear&nbsp;All

&gt;&gt;

&gt;&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;How&nbsp;can&nbsp;I&nbsp;determine&nbsp;the&nbsp;converged&nbsp;value&nbsp;of&nbsp;a&nbsp;simulation?

&gt;&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Because&nbsp;the&nbsp;pressure&nbsp;has&nbsp;big&nbsp;oscilations&nbsp;around&nbsp;it's

&gt;&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;converging&nbsp;value&nbsp;but&nbsp;it&nbsp;is&nbsp;difficult&nbsp;to&nbsp;determine&nbsp;that&nbsp;value.

&gt;&gt;

&gt;&gt;

&gt;&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Longer&nbsp;simulations&nbsp;on&nbsp;bigger&nbsp;systems.

&gt;&gt;

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

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

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

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

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

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

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

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

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

&gt;&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;mailto:gmx-users-request@gromacs.org&gt;.

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

&gt;&gt;

&gt;&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/20110410/ef6a449f/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;84,&nbsp;Issue&nbsp;81

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

</PRE>