[gmx-users] Free energy calculation
shuai lu
luai.cpu at gmail.com
Sun Apr 20 02:49:38 CEST 2008
Dear Justin,
Thank you very much for helping me again!
Best wishes!
2008/4/20, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org>:
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> Today's Topics:
>
> 1. Error of mdrun (s lal badshah)
> 2. Re: Error of mdrun (Mark Abraham)
> 3. Free energy calculation (shuai lu)
> 4. Re: Free energy calculation (Justin A. Lemkul)
> 5. Re: water can't freeze (Sagittarius)
> 6. Re: water can't freeze (Vasilii Artyukhov)
>
>
> ---------- 已转发邮件 ----------
> From: s lal badshah <shahbiochemist at yahoo.com>
> To: gromacs <gmx-users at gromacs.org>
> Date: Sat, 19 Apr 2008 12:12:27 +0100 (BST)
> Subject: [gmx-users] Error of mdrun
> Dear Mark,
> When I enter from root account the following is the result:
> linux:~ # which mdrun
> /sbin/mdrun
> linux:~ # which grompp
> /usr/bin/grompp
> linux:~ #
>
> But from user account the
> which mdrun
> usr/bin/mdrun
> and also the
> which grompp
> /usr/bin/grompp
> occured.
> 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.
> Regards,
> Lal badshah.
>
> Send instant messages to your online friends http://uk.messenger.yahoo.com
>
>
> ---------- 已转发邮件 ----------
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Date: Sun, 20 Apr 2008 00:15:09 +1000
> Subject: Re: [gmx-users] Error of mdrun
> s lal badshah wrote:
>
> > Dear Mark,
> > When I enter from root account the following is the result:
> > linux:~ # which mdrun
> > /sbin/mdrun
> > linux:~ # which grompp
> > /usr/bin/grompp
> > linux:~ #
> >
> > But from user account the
> > which mdrun
> > usr/bin/mdrun
> > and also the
> > which grompp
> > /usr/bin/grompp occured.
> > 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.
> >
>
> Don't ever use the root account for daily usage. It's like driving your
> car while you haven't finished major maintenance.
>
> 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.
>
> These problems have nothing to do with GROMACS, so you should consider
> alternative sources of information on the web.
>
> Mark
>
>
>
> ---------- 已转发邮件 ----------
> From: "shuai lu" <luai.cpu at gmail.com>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Date: Sat, 19 Apr 2008 22:13:52 +0800
> Subject: [gmx-users] Free energy calculation
>
> Hello everyone,
>
> 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
>
> or use g_lie by doing recepto-ligand-solvate md and ligand-solvate md
> separately?
>
> 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?
> For anther method, can the energy calculated by g_lie programme be
> thought as binding free energy?
>
> Thank you!
>
> --
> Lu Shuai
>
>
> ---------- 已转发邮件 ----------
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Date: Sat, 19 Apr 2008 10:47:21 -0400
> Subject: Re: [gmx-users] Free energy calculation
> Quoting shuai lu <luai.cpu at gmail.com>:
>
> > Hello everyone,
> >
> > 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
>
> Yes, among other things. Read the manual regarding all the free energy
> options.
> Simply setting free_energy = yes will not be everything you need to
> consider.
>
> >
> > or use g_lie by doing recepto-ligand-solvate md and ligand-solvate md
> > separately?
>
> g_lie will give you an estimate of free energy; I don't know how accurate
> it is
> relative to a rigorous thermodynamic integration procedure.
>
> >
> > 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?
>
> Check the mdrun output options (-dgdl)
>
> > For anther method, can the energy calculated by g_lie programme be
> thought
> > as binding free energy?
>
> Just as some general advice, search for Gromacs free energy tutorials.
> There is
> some good information on the wiki site, and there are some excellent
> tutorials
> out there, most notably one written by David Mobley. Many users have
> found
> this tutorial to be very informative.
>
> -Justin
>
> >
> > Thank you!
> >
> > --
> > Lu Shuai
> >
>
>
>
> ========================================
>
> 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/
>
> ========================================
>
>
>
> ---------- 已转发邮件 ----------
> From: Sagittarius <deckuofm at yahoo.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Date: Sat, 19 Apr 2008 07:41:46 -0700 (PDT)
> Subject: Re: [gmx-users] water can't freeze
>
> Send me please your files, I would like to have a look at them
>
>
>
> Alex
>
> --- On *Fri, 4/18/08, Wei, Xiupeng <xiupeng-wei at uiowa.edu>* wrote:
>
> From: Wei, Xiupeng <xiupeng-wei at uiowa.edu>
> Subject: [gmx-users] water can't freeze
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Date: Friday, April 18, 2008, 8:41 PM
>
> 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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> ---------- 已转发邮件 ----------
> From: "Vasilii Artyukhov" <darth.vasya at gmail.com>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Date: Sat, 19 Apr 2008 21:17:27 +0400
> Subject: Re: [gmx-users] water can't freeze
> Dear Xiupeng,
>
> What you're seeing is the difference between freezing water and overcooling
> 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 :)
>
> Best regards,
> Vasilii
>
> 2008/4/19, Wei, Xiupeng <xiupeng-wei at uiowa.edu>:
> >
> > 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
> >
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> > posting!
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> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
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>
--
卢帅
Lu Shuai
中国药科大学
China Pharmaceutical University
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