<DIV> Hi Justin,</DIV>
<DIV> </DIV>
<DIV>Thanks so much for your prompt response. If using AMBER force field, can one construct the parameters of non-standard molecules through ANTECHAMBER in AMBER package? </DIV>
<DIV> </DIV>
<DIV>Thanks in advance.</DIV>
<DIV>Have a nice day.</DIV>
<DIV> </DIV>
<DIV>---</DIV>
<DIV>Jeffrey</DIV>
<DIV> </DIV>
<DIV>>Message: 3<BR>>Date: Mon, 06 Oct 2008 07:03:58 -0400<BR>>From: "Justin A. Lemkul" <JALEMKUL><BR>>Subject: Re: [gmx-users] some questions about gromacs<BR>>To: Discussion list for GROMACS users <GMX-USERS><BR>>Message-ID: <48E9F09E.7040308@vt.edu><BR>>Content-Type: text/plain; charset=UTF-8; format=flowed<BR>><BR>><BR>><BR>>dcip1101 wrote:<BR>>> Dear all,<BR>>> <BR>>> I am a new user of Gromacs. To start my job, I am confused by several <BR>>> questions about GROMACS and requesting the answers.<BR>>> <BR>>> 1. Can one use amber force field in gromacs?<BR>><BR>>Yes. See http://chemistry.csulb.edu/ffamber/ and follow the usage instructions <BR>>carefully.<BR>><BR>>> 2. How to prepare parameters for a cofactor not included in the standard <BR>>> force fields?<BR>><BR>>This is a very advanced topic. See here:<BR>><BR>>http://wiki.gromacs.org/index.php/Parameterization<BR>><BR>>> 3. Any further suggestions to a new user to use the package better?<BR>>> <BR>><BR>>Depends on what you are doing. Read lots of tutorials and consult the mailing <BR>>list archive and wiki site (wiki.gromacs.org) if you have problems or are not <BR>>certain how to implement certain features.<BR>><BR>>-Justin<BR>><BR>>> <BR>>> Thanks so much for your time.<BR>>> Have a nice day.<BR>>> <BR>>> ----<BR>>> Jeffrey <BR>>> <BR>>> <BR></GMX-USERS></JALEMKUL></DIV>
<DIV> </DIV>
<DIV></DIV><BR><PRE>在2008-10-06，gmx-users-request@gromacs.org 写道：
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>Today's Topics:
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> 1. some questions about gromacs (dcip1101)
> 2. RE: Heat Flux and Lambda (Berk Hess)
> 3. Re: some questions about gromacs (Justin A. Lemkul)
> 4. Re: Pull.pdo Columns (Thomas Schlesier)
> 5. Re: steady (Justin A. Lemkul)
> 6. questions about using GROMACS (dcip1101)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Mon, 6 Oct 2008 17:52:45 +0800 (CST)
>From: dcip1101 <DCIP1101 some="" questions="" about="" gromacs="" gmx-users="" text="" plain="" charset="gbk" Dear="" all="" I="" am="" a="" new="" user="" of="" Gromacs.="" To="" start="" my="" job="" I="" am="" confused="" by="" several="" questions="" about="" GROMACS="" and="" requesting="" the="" answers.="" Can="" one="" use="" amber="" force="" field="" in="" gromacs="" How="" to="" prepare="" parameters="" for="" a="" cofactor="" not="" included="" in="" the="" standard="" force="" fields="" Any="" further="" suggestions="" to="" a="" new="" user="" to="" use="" the="" package="" better="" so="" much="" for="" your="" time.="" a="" nice="" day.="" next="" part="" HTML="" attachment="" was="" scrubbed...="" http:="" www.gromacs.org="" pipermail="" gmx-users="" attachments="" attachment-0001.html="" Mon="" Oct="" Berk="" Hess=""><GMX3 RE:="" Heat="" Flux="" and="" Lambda="" Discussion="" list="" for="" GROMACS="" users=""><GMX-USERS><BLU134-W25AFB70997D41EEFFC65638E390 text="" plain="" charset="iso-8859-1" Date:="" Fri="" Oct="" From:="" spoel="" To:="" gmx-users="" Subject:="" Re:="" Heat="" Flux="" and="" Lambda="" Andy="" Shelley="" wrote:="" David="" I="" looked="" up="" the="" euqation="" for="" the="" Nose-Hoover="" thermostat="" and="" don="" understand="" where="" lambda="" comes="" from="" and="" how="" to="" use="" the="" number="" of="" degreees="" of="" freedom="" to="" determine="" the="" heat="" flux="" of="" a="" group.="" Could="" you="" explain="" some="" more="" Aha="" this="" only="" works="" for="" Berendsen="" I="" would="" think.="" same="" equation="" might="" not="" work="" but="" one="" can="" do="" something="" similar.="" velocities="" are="" scaled="" each="" step="" by="" lambda="" which="" you="" can="" get="" with="" g_energy.="" heat="" flux="" per="" degree="" of="" freedom="" is="" therefore="" simply:="" number="" of="" degrees="" of="" freedom="" for="" temperature="" coupling="" groups="" is="" printed="" at="" the="" beginning="" of="" the="" log="" file.="" Thanks="" Andy="" I="" have="" been="" reading="" through="" the="" mailing="" list="" and="" have="" read="" some="" discussion="" that="" heat="" flux="" can="" be="" indicated="" by="" the="" value="" of="" lambda.="" Can="" I="" calculate="" the="" amount="" of="" heat="" flux="" from="" the="" lambda="" value="" In="" principle="" yes.="" Look="" up="" the="" equation="" for="" the="" temperature="" coupling.="" You="" will="" need="" to="" know="" the="" number="" of="" degrees="" of="" freedom="" as="" printed="" in="" md.log="" file.="" Thanks="" Andy="" Shelley="" _______________________________________________="" gmx-users="" mailing="" list="" gmx-users=""><mailto:gmx-users http:="" www.gromacs.org="" mailman="" listinfo="" gmx-users="" Please="" search="" the="" archive="" at="" http:="" www.gromacs.org="" search="" before="" posting="" Please="" don="" post="" requests="" to="" the="" list.="" Use="" the="" www="" interface="" or="" send="" it="" to="" gmx-users-request=""><mailto:gmx-users-request Can="" post="" Read="" http:="" www.gromacs.org="" mailing_lists="" users.php="" David.="" ________________________________________________________________________="" David="" van="" der="" Spoel="" PhD="" Professor="" of="" Biology="" Dept.="" of="" Cell="" and="" Molecular="" Biology="" Uppsala="" University.="" Husargatan="" Box="" Uppsala="" Sweden="" phone:="" fax:="" spoel=""><mailto:spoel spoel=""><mailto:spoel http:="" folding.bmc.uu.se=""><HTTP: folding.bmc.uu.se="">
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>> David.
>> ________________________________________________________________________
>> David van der Spoel, PhD, Professor of Biology
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596, 75124 Uppsala, Sweden
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>------------------------------
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>Message: 3
>Date: Mon, 06 Oct 2008 07:03:58 -0400
>From: "Justin A. Lemkul" <JALEMKUL Re:="" some="" questions="" about="" gromacs="" Discussion="" list="" for="" GROMACS="" users=""><GMX-USERS text="" plain="" charset="UTF-8;" format="flowed" wrote:="" Dear="" all="" I="" am="" a="" new="" user="" of="" Gromacs.="" To="" start="" my="" job="" I="" am="" confused="" by="" several="" questions="" about="" GROMACS="" and="" requesting="" the="" answers.="" Can="" one="" use="" amber="" force="" field="" in="" gromacs="" See="" http:="" chemistry.csulb.edu="" ffamber="" and="" follow="" the="" usage="" instructions="" How="" to="" prepare="" parameters="" for="" a="" cofactor="" not="" included="" in="" the="" standard="" force="" fields="" is="" a="" very="" advanced="" topic.="" See="" here:="" wiki.gromacs.org="" index.php="" Parameterization="" Any="" further="" suggestions="" to="" a="" new="" user="" to="" use="" the="" package="" better="" on="" what="" you="" are="" doing.="" Read="" lots="" of="" tutorials="" and="" consult="" the="" mailing="" archive="" and="" wiki="" site="" if="" you="" have="" problems="" or="" are="" not="" how="" to="" implement="" certain="" features.="" Thanks="" so="" much="" for="" your="" time.="" Have="" a="" nice="" day.="" Jeffrey="" ç=""><HTTP: link="" popme.163.com="">
>>
>>
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>--
>========================================
>
>Justin A. Lemkul
>Graduate Research Assistant
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu | (540) 231-9080
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>========================================
>
>
>------------------------------
>
>Message: 4
>Date: Mon, 6 Oct 2008 13:10:56 +0200
>From: Thomas Schlesier <SCHLESI Re:="" Pull.pdo="" Columns=""><GMX-USERS text="" plain="" charset="ISO-8859-15" Message:="" Date:="" Sun="" Oct="" From:="" HARIHARAN=""><VUH105 Subject:="" Pull.pdo="" Columns="" To:="" Discussion="" list="" for="" GROMACS="" users=""><GMX-USERS Message-ID:="" Content-Type:="" text="" plain="" charset="utf-8" Hello="" I="" understand="" this="" topic="" has="" been="" dealt="" with="" previously="" and="" I="" have="" read="" all="" the="" relative="" material="" from="" the="" archives="" but="" I="" am="" still="" having="" trouble="" deciphering="" what="" each="" column="" corresponds="" to="" in="" the="" pull.pdo="" file="" for="" an="" AFM="" pull="" with="" one="" pull="" group="" and="" one="" reference="" group="" and="" pulling="" in="" only="" the="" X="" direction.="" From="" what="" I="" read="" the="" columns="" are="" as="" follows:="" Time="" RefX="" RefY="" RefZ="" PullX="" PullY="" PullZ="" SpringX="" SpringY="" SpringZ="" columns="" should="" be="" GORMACS="" RefX="" RefY="" RefZ="" PullX="" SprX="" PullY="" SprY="" PullZ="" SprZ="" can="" check="" this="" the="" pulldir="" should="" be="" SprX="" and="" so="" on...="" a="" total="" of="" columns.="" The="" problem="" is="" that="" when="" I="" use="" the="" values="" of="" for="" the="" reference="" group="" and="" pull="" group="" at="" time="" zero="" to="" calculate="" end="" to="" end="" distance="" they="" do="" not="" correspond="" to="" my="" starting="" pdb="" file="" after="" solvation.="" Any="" thoughts="" ______________________________="" Venkatesh="" Hariharan="" Pennsylvania="" State="" University="" Schreyer="" Honors="" College="" Undergraduate="" Bioengineering="" must="" be="" the="" change="" you="" wish="" to="" see="" in="" the="" world.="" Karamchand="" Gandhi="" next="" part="" An="" HTML="" attachment="" was="" scrubbed...="" URL:="" http:="" www.gromacs.org="" pipermail="" gmx-users="" attachments="" attachment-0001.html="" Mon="" Oct="" A.="" Lemkul=""><JALEMKUL Re:="" steady="" Discussion="" list="" for="" GROMACS="" users=""><GMX-USERS text="" plain="" charset="ISO-8859-1;" format="flowed" karbalaee="" wrote:="" hi="" justin="" in="" during="" making="" mix="" solvent="" for="" example="" after="" making="" box="" I="" use="" trjconv="" pdb="" file="" lost="" the="" the="" arrange="" and="" it="" need="" long="" time="" for="" equilbrate="" and="" steady="" density.Is="" it="" right="" or="" any="" suggestion="" about="" it="" option="" are="" you="" giving="" trjconv="" nojump="" etc.="" Why="" do="" you="" need="" If="" your="" goal="" is="" to="" create="" a="" mixed="" solvent="" simply="" using="" normal="" periodic="" conditions="" during="" the="" simulation="" should="" be="" all="" you="" need.="" will="" likely="" give="" you="" a="" distorted="" unit="" cell.="" thanks="" A.="" Lemkul="" Research="" Assistant="" of="" Biochemistry="" Tech="" VA="" www.bevanlab.biochem.vt.edu="" Pages="" Personal="" justin="" Mon="" Oct="" dcip1101=""><DCIP1101 questions="" about="" using="" GROMACS="" gmx-users="" text="" plain="" charset="gbk" Dear="" all="" I="" am="" a="" new="" user="" of="" Gromacs.="" To="" start="" my="" job="" I="" am="" confused="" by="" several="" questions="" about="" GROMACS="" and="" requesting="" the="" answers.="" Can="" one="" use="" amber="" force="" field="" in="" gromacs="" How="" to="" prepare="" parameters="" for="" a="" cofactor="" not="" included="" in="" the="" standard="" force="" fields="" Any="" further="" suggestions="" to="" a="" new="" user="" to="" use="" the="" package="" better="" so="" much="" for="" your="" time.="" a="" nice="" day.="" mailing="" list="" www.gromacs.org="" mailman="" listinfo="" gmx-users="" search="" the="" archive="" at="" http:="" www.gromacs.org="" search="" before="" posting="" of="" gmx-users="" Digest="" Vol="" Issue="" next="" part="" HTML="" attachment="" was="" scrubbed...="" http:="" www.gromacs.org="" pipermail="" gmx-users="" attachments="" b3563d7c="" attachment.html="" mailing="" list="" www.gromacs.org="" mailman="" listinfo="" gmx-users="" search="" the="" archive="" at="" http:="" www.gromacs.org="" search="" before="" posting="" of="" gmx-users="" Digest="" Vol="" Issue=""></DCIP1101></GMX-USERS></JALEMKUL></GMX-USERS></VUH105></GMX-USERS></SCHLESI></HTTP:></GMX-USERS></JALEMKUL></HTTP:></mailto:spoel></mailto:spoel></mailto:gmx-users-request></mailto:gmx-users></BLU134-W25AFB70997D41EEFFC65638E390></GMX-USERS></GMX3></DCIP1101></PRE><br><!-- footer --><br>
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