<div>Dear Justin,</div>
<div> </div>
<div>Thank you very much for helping me again!</div>
<div>Best wishes!<br><br> </div>
<div><span class="gmail_quote">2008/4/20, <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> <<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
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<br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of gmx-users digest..."<br> </div><br>Today's Topics:<br><br> 1. Error of mdrun (s lal badshah)<br> 2. Re: Error of mdrun (Mark Abraham)<br>
3. Free energy calculation (shuai lu)<br> 4. Re: Free energy calculation (Justin A. Lemkul)<br> 5. Re: water can't freeze (Sagittarius)<br> 6. Re: water can't freeze (Vasilii Artyukhov)<br><br><br>---------- 已转发邮件 ----------<br>
From: s lal badshah <<a href="mailto:shahbiochemist@yahoo.com">shahbiochemist@yahoo.com</a>><br>To: gromacs <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Date: Sat, 19 Apr 2008 12:12:27 +0100 (BST)<br>
Subject: [gmx-users] Error of mdrun<br>Dear Mark,<br>When I enter from root account the following is the result:<br><span style="FONT-WEIGHT: bold">linux:~ # which mdrun</span><br style="FONT-WEIGHT: bold"><span style="FONT-WEIGHT: bold">/sbin/mdrun</span><br style="FONT-WEIGHT: bold">
<span style="FONT-WEIGHT: bold">linux:~ # which grompp</span><br style="FONT-WEIGHT: bold"><span style="FONT-WEIGHT: bold">/usr/bin/grompp</span><br style="FONT-WEIGHT: bold"><span style="FONT-WEIGHT: bold">linux:~ # </span><br>
<br>But from user account the<br> <span style="FONT-WEIGHT: bold">which mdrun</span><br style="FONT-WEIGHT: bold"><span style="FONT-WEIGHT: bold">usr/bin/mdrun</span> <br>and also the<br> <span style="FONT-WEIGHT: bold">which grompp</span><br style="FONT-WEIGHT: bold">
<span style="FONT-WEIGHT: bold">/usr/bin/grompp</span> <br>occured.<br>Actually I have very little experience with linux.I install VMD which didn't open in user account but opened only in root account so I do MD simulation in root accounts.If I do Md simulation from user account is this problem arises or not? Is there any command so that mdrun also operate in root account? A few mentioned in past mails archive of gromacs didn't work as I used them.<br>
Regards,<br>Lal badshah.<br>
<p>Send instant messages to your online friends <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://uk.messenger.yahoo.com/" target="_blank">http://uk.messenger.yahoo.com</a> </p><br><br>---------- 已转发邮件 ----------<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Date: Sun, 20 Apr 2008 00:15:09 +1000<br>
Subject: Re: [gmx-users] Error of mdrun<br>s lal badshah wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px; BORDER-LEFT: #ccc 1px solid">Dear Mark,<br>When I enter from root account the following is the result:<br>linux:~ # which mdrun<br>/sbin/mdrun<br>linux:~ # which grompp<br>
/usr/bin/grompp<br>linux:~ #<br><br>But from user account the<br> which mdrun<br>usr/bin/mdrun<br>and also the<br> which grompp<br>/usr/bin/grompp occured.<br>Actually I have very little experience with linux.I install VMD which didn't open in user account but opened only in root account so I do MD simulation in root accounts.If I do Md simulation from user account is this problem arises or not? Is there any command so that mdrun also operate in root account? A few mentioned in past mails archive of gromacs didn't work as I used them.<br>
</blockquote><br>Don't ever use the root account for daily usage. It's like driving your car while you haven't finished major maintenance.<br><br>If you follow the VMD installation instructions properly, it will work from user accounts, as with any other decent software. You should fix the cause of the VMD problem, or you'll only create more problems for yourself - such as the above. That said, you'll probably struggle to actually fix the existing consequences of your root usage... so re-installing the OS and starting again is a serious option.<br>
<br>These problems have nothing to do with GROMACS, so you should consider alternative sources of information on the web.<br><br>Mark<br><br><br><br>---------- 已转发邮件 ----------<br>From: "shuai lu" <<a href="mailto:luai.cpu@gmail.com">luai.cpu@gmail.com</a>><br>
To: "Discussion list for GROMACS users" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Date: Sat, 19 Apr 2008 22:13:52 +0800<br>Subject: [gmx-users] Free energy calculation<br>
<div> </div>
<div>Hello everyone,</div>
<div> </div>
<div>Here i want to caculate the binding free energy between an ligand and its receptor. Should I set free_energy as "yes" in Free Energy Perturbation Part </div>
<div>or use g_lie by doing recepto-ligand-solvate md and ligand-solvate md separately?</div>
<div> </div>
<div>If run a md by set free_energy as "yes", how shoud i get free energy, just by g_energy alone or with some special parameter?</div>
<div>For anther method, can the energy calculated by g_lie programme be thought as binding free energy?</div>
<div> </div>
<div>Thank you!<br clear="all"><br>-- <br>Lu Shuai</div><br><br>---------- 已转发邮件 ----------<br>From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Date: Sat, 19 Apr 2008 10:47:21 -0400<br>Subject: Re: [gmx-users] Free energy calculation<br>Quoting shuai lu <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:luai.cpu@gmail.com">luai.cpu@gmail.com</a>>:<br>
<br>> Hello everyone,<br>><br>> Here i want to caculate the binding free energy between an ligand and its<br>> receptor. Should I set free_energy as "yes" in Free Energy Perturbation Part<br><br>Yes, among other things. Read the manual regarding all the free energy options.<br>
Simply setting free_energy = yes will not be everything you need to consider.<br><br>><br>> or use g_lie by doing recepto-ligand-solvate md and ligand-solvate md<br>> separately?<br><br>g_lie will give you an estimate of free energy; I don't know how accurate it is<br>
relative to a rigorous thermodynamic integration procedure.<br><br>><br>> If run a md by set free_energy as "yes", how shoud i get free energy, just<br>> by g_energy alone or with some special parameter?<br>
<br>Check the mdrun output options (-dgdl)<br><br>> For anther method, can the energy calculated by g_lie programme be thought<br>> as binding free energy?<br><br>Just as some general advice, search for Gromacs free energy tutorials. There is<br>
some good information on the wiki site, and there are some excellent tutorials<br>out there, most notably one written by David Mobley. Many users have found<br>this tutorial to be very informative.<br><br>-Justin<br><br>
><br>> Thank you!<br>><br>> --<br>> Lu Shuai<br>><br><br><br><br>========================================<br><br>Justin A. Lemkul<br>Graduate Research Assistant<br>Department of Biochemistry<br>Virginia Tech<br>
Blacksburg, VA<br><a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> | (540) 231-9080<br><a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/</a><br>
<br>========================================<br><br><br><br>---------- 已转发邮件 ----------<br>From: Sagittarius <<a href="mailto:deckuofm@yahoo.com">deckuofm@yahoo.com</a>><br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Date: Sat, 19 Apr 2008 07:41:46 -0700 (PDT)<br>Subject: Re: [gmx-users] water can't freeze<br>
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<p>Send me please your files, I would like to have a look at them</p>
<p> </p>
<p>Alex<br><br>--- On <b>Fri, 4/18/08, Wei, Xiupeng <i><<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:xiupeng-wei@uiowa.edu" target="_blank">xiupeng-wei@uiowa.edu</a>></i></b> wrote:<br></p>
<blockquote style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid">From: Wei, Xiupeng <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:xiupeng-wei@uiowa.edu" target="_blank">xiupeng-wei@uiowa.edu</a>><br>
Subject: [gmx-users] water can't freeze<br>To: "<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>" <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Date: Friday, April 18, 2008, 8:41 PM<br><br><pre>Hi gmx users,
I'm a new Gromacs user. Till now, I can get pretty good simulation
of ice melting to water, but why can't I simulate water freezing to ice?
The .top and .gro files used for water freezing simulation are
generated by ice melting to 310K. I changed the temperature in .mdp file to
230K, but after mdrun, the water was still water, it can't freeze?
How can I get water freezing to ice?
I paste mdp for your reference.
Thanks.
best,
xiupeng
title = icing at 230 K with cuffoff
cpp = /lib/cpp
integrator = md
;Time step
dt = 0.002
nsteps = 100000
;Output control
nstxout = 100000
nstvout = 100000
nstlog = 100
nstenergy = 100
nstxtcout = 100
;Neigbour searching
nstlist = 10
ns_type = grid
rlist = 0.8
;Non bonded interaction
coulombtype = pme
optimize_fft = yes
fourierspacing = 0.2
pme-order = 6
ewald-rtol = 1e-05
rcoulomb = 0.8
vdw-type = Cut-off
rvdw = 0.8
DispCorr = EnerPres
;Temperature coupling
tcoupl = berendsen
tc-grps = System
tau_t = 0.1
ref_t = 230
;Pressure coupling
pcoupl = berendsen
pcoupltype = isotropic
tau_p = 1.0
compressibility = 5e-5
ref_p = 1.0
gen_temp = 230.0
constraints = all-bonds
; generate velocities
gen_vel = yes
gen_seed = 173529
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<br>---------- 已转发邮件 ----------<br>From: "Vasilii Artyukhov" <<a href="mailto:darth.vasya@gmail.com">darth.vasya@gmail.com</a>><br>To: "Discussion list for GROMACS users" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Date: Sat, 19 Apr 2008 21:17:27 +0400<br>Subject: Re: [gmx-users] water can't freeze<br>Dear Xiupeng,<br><br>What you're seeing is the difference between <span style="FONT-STYLE: italic">freezing </span>water and <span style="FONT-STYLE: italic">overcooling </span>it. If you want your water to crystallize, you'll actually have to make it - e.g., by putting it in contact with ice. Normally, pure water doesn't freeze on its own, you can easily verify this experimentally at home :)<br>
<br>Best regards,<br>Vasilii<br><br>
<div><span class="gmail_quote">2008/4/19, Wei, Xiupeng <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:xiupeng-wei@uiowa.edu" target="_blank">xiupeng-wei@uiowa.edu</a>>:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid">Hi gmx users,<br> I'm a new Gromacs user. Till now, I can get pretty good simulation of ice melting to water, but why can't I simulate water freezing to ice?<br>
The .top and .gro files used for water freezing simulation are generated by ice melting to 310K. I changed the temperature in .mdp file to 230K, but after mdrun, the water was still water, it can't freeze?<br>
How can I get water freezing to ice?<br> I paste mdp for your reference.<br> Thanks.<br><br>best,<br>xiupeng<br><br><br>title = icing at 230 K with cuffoff<br>cpp = /lib/cpp<br>
integrator = md<br>;Time step<br>dt = 0.002<br>nsteps = 100000<br>;Output control<br>nstxout = 100000<br>nstvout = 100000<br>nstlog = 100<br>
nstenergy = 100<br>nstxtcout = 100<br>;Neigbour searching<br>nstlist = 10<br>ns_type = grid<br>rlist = 0.8<br>;Non bonded interaction<br>coulombtype = pme<br>
optimize_fft = yes<br>fourierspacing = 0.2<br>pme-order = 6<br>ewald-rtol = 1e-05<br>rcoulomb = 0.8<br>vdw-type = Cut-off<br>rvdw = 0.8<br>
DispCorr = EnerPres<br>;Temperature coupling<br>tcoupl = berendsen<br>tc-grps = System<br>tau_t = 0.1<br>ref_t = 230<br>;Pressure coupling<br>
pcoupl = berendsen<br>pcoupltype = isotropic<br>tau_p = 1.0<br>compressibility = 5e-5<br>ref_p = 1.0<br><br>gen_temp = 230.0<br>
constraints = all-bonds<br>; generate velocities<br>gen_vel = yes<br>gen_seed = 173529<br><br><br>_______________________________________________<br>gmx-users mailing list <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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Please search the archive at <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br></blockquote></div><br><br clear="all">
<br>-- <br>卢帅<br>Lu Shuai <br>中国药科大学<br>China Pharmaceutical University