Dear Justin, Thank you very much for helping me again! Best wishes!
2008/4/20, [EMAIL PROTECTED] <[EMAIL PROTECTED]>: > > Send gmx-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > [EMAIL PROTECTED] > > You can reach the person managing the list at > [EMAIL PROTECTED] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > 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 <[EMAIL PROTECTED]> > To: gromacs <[email protected]> > 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 <[EMAIL PROTECTED]> > To: Discussion list for GROMACS users <[email protected]> > 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" <[EMAIL PROTECTED]> > To: "Discussion list for GROMACS users" <[email protected]> > 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" <[EMAIL PROTECTED]> > To: Discussion list for GROMACS users <[email protected]> > Date: Sat, 19 Apr 2008 10:47:21 -0400 > Subject: Re: [gmx-users] Free energy calculation > Quoting shuai lu <[EMAIL PROTECTED]>: > > > 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 > [EMAIL PROTECTED] | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > ======================================== > > > > ---------- 已转发邮件 ---------- > From: Sagittarius <[EMAIL PROTECTED]> > To: Discussion list for GROMACS users <[email protected]> > 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 <[EMAIL PROTECTED]>* wrote: > > From: Wei, Xiupeng <[EMAIL PROTECTED]> > Subject: [gmx-users] water can't freeze > To: "[email protected]" <[email protected]> > 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 > > > _______________________________________________ > gmx-users mailing list [EMAIL > PROTECTED]://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > ------------------------------ > Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it > now.<http://us.rd.yahoo.com/evt=51733/*http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ> > > ---------- 已转发邮件 ---------- > From: "Vasilii Artyukhov" <[EMAIL PROTECTED]> > To: "Discussion list for GROMACS users" <[email protected]> > 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 <[EMAIL PROTECTED]>: > > > > 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 [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > _______________________________________________ > gmx-users mailing list > [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > -- 卢帅 Lu Shuai 中国药科大学 China Pharmaceutical University
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