[gmx-users] sorry, that wasn't for you!!!!
Hernan Alonso
hernan.alonso at anu.edu.au
Tue Sep 30 04:35:01 CEST 2003
On Mon, 2003-09-29 at 20:00, gmx-users-request at gromacs.org wrote:
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> Today's Topics:
>
> 1. Re: convert pdb to gro file? (Xavier Periole)
> 2. how big the difference between two ligand can FEP handle?] (QZ)
> 3. Re: Simple L-J Particles' simulation (Jia-Lin Lo)
> 4. Re: Simple L-J Particles' simulation (David)
> 5. Re: g_gyrate (Anton Feenstra)
> 6. Re: free energy for converting DUM into Ar (Anton Feenstra)
> 7. Re: Simple L-J Particles' simulation (Anton Feenstra)
> 8. Re: [Fwd: help me please] (Anton Feenstra)
> 9. Re: Regd. no PBC (Anton Feenstra)
> 10. Re: Simple L-J Particles' simulation (Lieven Buts)
>
> --__--__--
>
> Message: 1
> Date: Sun, 28 Sep 2003 05:23:25 -0400
> Subject: Re: [gmx-users] convert pdb to gro file?
> From: Xavier Periole <Xavier.Periole at physbio.mssm.edu>
> To: gmx-users at gromacs.org
> Reply-To: gmx-users at gromacs.org
>
>
>
> Your system is not a conventional "protein". I don't think that
> Cobalt is defined in the topology. And you have two small
> molecules that way too strange to be understood.
> Try to define you topology by hand or using PRODRG
> program.
>
>
> XAvier
>
>
> --__--__--
>
> Message: 2
> Date: Sun, 28 Sep 2003 21:01:24 -0500
> From: QZ <qzou at iupui.edu>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] how big the difference between two ligand can FEP handle?]
> Reply-To: gmx-users at gromacs.org
>
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> Dear All,
> I am learning to use FEP to get the bind free energy difference between
> two totally different ligands bound a protein. The number of atoms
> varies between the ligands. Does gromacs require the same number of
> atoms between sytem A and B? If not, how does the interpolation work
> between the ligands with different atom numbers? Should I use dummy
> atoms to match the atom numbers between the ligands? Thanks for any input.
>
> Q. Zou , Ph D.
> Indiana University
>
>
>
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> <pre>Dear All,
> I am learning to use FEP to get the bind free energy difference between
> two totally different ligands bound a protein. The number of atoms
> varies between the ligands. Does gromacs require the same number of
> atoms between sytem A and B? If not, how does the interpolation work
> between the ligands with different atom numbers? Should I use dummy
> atoms to match the atom numbers between the ligands? Thanks for any input.
>
> Q. Zou , Ph D.
> Indiana University
>
>
> </pre>
> </body>
> </html>
>
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>
> --__--__--
>
> Message: 3
> From: "Jia-Lin Lo" <jllo at phy.ncu.edu.tw>
> To: <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Simple L-J Particles' simulation
> Date: Mon, 29 Sep 2003 11:49:43 +0800
> Reply-To: gmx-users at gromacs.org
>
>
> Hi, David and gmx-users:
> I read your grop1.mdp file and follow the procedure you told Albert.
> I am curious about some parameters in your mdp file. As to " General-Born
> electricstatics"
> and " Implicit solvation", Can gromacs really do these setting?
> When I look at "mdout.mdp" file produced by grop1.md file. It's a mdp
> file I am familiar with.
> But these parameters " GB electricstatics" and " Implicit solvation" are
> missing.
> I am confused about these 2 mdp files. Could you explain the
> differences ? Thanks in advance.
>
> Best Regards
> Jialin
>
> > yes:
> > run grompp once
> > then
> > mv mdout.mdp grompp.mdp
> > and edit that as you like.
> >
> > >
> > >
> > > David.
> > > ________________________________________________________________________
> > > David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> > > Dept. of Cell and Molecular Biology, Uppsala University.
> > > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > > phone: 46 18 471 4205 fax: 46 18 511 755
> > > spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
>
>
> --__--__--
>
> Message: 4
> Subject: Re: [gmx-users] Simple L-J Particles' simulation
> From: David <spoel at xray.bmc.uu.se>
> To: gmx-users at gromacs.org
> Organization:
> Date: 29 Sep 2003 10:07:13 +0200
> Reply-To: gmx-users at gromacs.org
>
> On Mon, 2003-09-29 at 05:49, Jia-Lin Lo wrote:
> > Hi, David and gmx-users:
> > I read your grop1.mdp file and follow the procedure you told Albert.
> > I am curious about some parameters in your mdp file. As to " General-Born
> > electricstatics"
> > and " Implicit solvation", Can gromacs really do these setting?
> > When I look at "mdout.mdp" file produced by grop1.md file. It's a mdp
> > file I am familiar with.
> > But these parameters " GB electricstatics" and " Implicit solvation" are
> > missing.
> > I am confused about these 2 mdp files. Could you explain the
> > differences ? Thanks in advance.
> >
>
> In the next release...
>
> > Best Regards
> > Jialin
> >
> > > yes:
> > > run grompp once
> > > then
> > > mv mdout.mdp grompp.mdp
> > > and edit that as you like.
> > >
> > > >
> > > >
> > > > David.
> > > > ________________________________________________________________________
> > > > David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> > > > Dept. of Cell and Molecular Biology, Uppsala University.
> > > > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > > > phone: 46 18 471 4205 fax: 46 18 511 755
> > > > spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> > > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > >
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
> --__--__--
>
> Message: 5
> Date: Fri, 26 Sep 2003 18:12:36 +0200
> From: Anton Feenstra <feenstra at chem.vu.nl>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] g_gyrate
> Reply-To: gmx-users at gromacs.org
>
> David wrote:
> > On Fri, 2003-09-26 at 03:55, Dallas Warren wrote:
> >
> >>David,
> >>
> >>
> >>>just periodic boundary conditions.
> >>
> >>OK, thought that might be the other possible thing causing problems.
> >>
> >>This pops up a bit I have noticed. For the developers, is it possible
> >>to integrate support of the pbc into these scripts? I know there are
> >>a few tricks to get them supporting the pbc, but have no idea if it
> >>will fit in with the various GROMACS scripts. A colleague here has
> >>implemented it into a package of Perl scripts that he has written to
> >>manipulate various simulation files.
> >
> > It is *possible* of course. One would just have to call the routines
> > that are already in trjconv. But it's work...
>
> You can still first do it 'manually' with trjconv, with the added advantage
> that it only has to be done once, and you can check if it is done the way
> you expect it to. Having said that, the last time I tried either -pbc nojump,
> or the 'cluster' option, it didn't work the way I expected (but I also did
> not have time then to get to the bottom of it).
>
>
> --
> Groetjes,
>
> Anton
> _____________ _______________________________________________________
> | | |
> | _ _ ___,| K. Anton Feenstra |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
> | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
> | | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
> | | "If You See Me Getting High, Knock Me Down" |
> | | (Red Hot Chili Peppers) |
> |_____________|_______________________________________________________|
>
>
>
> --__--__--
>
> Message: 6
> Date: Mon, 29 Sep 2003 07:33:53 +0200
> From: Anton Feenstra <feenstra at chem.vu.nl>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] free energy for converting DUM into Ar
> Reply-To: gmx-users at gromacs.org
>
> Ilya Chorny wrote:
> > I figured it out.
>
> Perhaps, for the sake of those searching the archives for answers,
> you could post a short summary of what you did?
>
>
> --
> Groetjes,
>
> Anton
> _____________ _______________________________________________________
> | | |
> | _ _ ___,| K. Anton Feenstra |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
> | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
> | | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
> | | "If You See Me Getting High, Knock Me Down" |
> | | (Red Hot Chili Peppers) |
> |_____________|_______________________________________________________|
>
>
>
> --__--__--
>
> Message: 7
> Date: Mon, 29 Sep 2003 07:36:44 +0200
> From: Anton Feenstra <feenstra at chem.vu.nl>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Simple L-J Particles' simulation
> Reply-To: gmx-users at gromacs.org
>
> David wrote:
> > On Sat, 2003-09-27 at 16:33, Albert Sun wrote:
> >
> >>Hi, David,
> >>Thank you for your reply.
> >>I did as you advised, run grompp once and
> >> mv mdout.mdp grompp.mdp
> >>but get " bad comment or file name "
> >
> > Oh dear, I hope you're not running windows. Please upgrade to Linux in
> > that case, otherwise check spelling.
>
> The intent of David's command is to change the name of 'mdout.mdp'.
> By the way, if you look carefully at the messages grompp displays
> about unknown parameters, you'll find that often also useful hints
> are given.
>
>
> --
> Groetjes,
>
> Anton
> _____________ _______________________________________________________
> | | |
> | _ _ ___,| K. Anton Feenstra |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
> | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
> | | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
> | | "If You See Me Getting High, Knock Me Down" |
> | | (Red Hot Chili Peppers) |
> |_____________|_______________________________________________________|
>
>
>
> --__--__--
>
> Message: 8
> Date: Mon, 29 Sep 2003 07:53:21 +0200
> From: Anton Feenstra <feenstra at chem.vu.nl>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] [Fwd: help me please]
> Reply-To: gmx-users at gromacs.org
>
> sunzhmd at mail.ustc.edu.cn wrote:
> > Hi all,
> >
> > I download a pdb file of DEOXYRIBONUCLEIC ACID with many records.Then I
> > want to convert it into a gromacs structure file .gro by the
> > command
> >
> > pdb2gmx -f filename.pdb
> >
> > Then a error was encountered which reads
> >
> > Residue 'A' not found in residue topology file database
>
> DNA/RNA are not very well implemented and supported. However, many people
> have been workin on it recently. Check the archives for the latest
> developments, as well as hints for the basic set-up of D/RNA simulations.
>
> > I do not know why. I wonder if you can do me a favor and help me with this
> > question.
> >
> > By the way, I am a new guy to gromacs. So I wonder if you can tell me
> > which records are useful in a officially distributed standard pdb file, as
> > far as md simulation is concerned. Are there any differences in format
> > between a pdb file that can be handled by pdb2gmx and a officially
> > distributed standard pdb file.
>
> Basicall, the only fields pdb2gmx cares about are 'ATOM' and 'HETATM",
> the rest is simply ignored. The format is identical to the 'official' one.
>
>
> --
> Groetjes,
>
> Anton
> _____________ _______________________________________________________
> | | |
> | _ _ ___,| K. Anton Feenstra |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
> | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
> | | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
> | | "If You See Me Getting High, Knock Me Down" |
> | | (Red Hot Chili Peppers) |
> |_____________|_______________________________________________________|
>
>
>
> --__--__--
>
> Message: 9
> Date: Mon, 29 Sep 2003 07:56:37 +0200
> From: Anton Feenstra <feenstra at chem.vu.nl>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Regd. no PBC
> Reply-To: gmx-users at gromacs.org
>
> David wrote:
> > On Fri, 2003-09-26 at 22:16, Anjan Raghunathan wrote:
> >
> >>Hi,
> >> I'd like to know how the No Periodic Boundary Condition switch works. Does it blow up the system over time when dealing with electrostatic systems?Does the box size get updated every time step?Or is there some scheme to maintain the constant box size?
> >>
> >
> > it's a vacuum simulation, so your atoms/molecule may evaporate. box is
> > not used for anything and e.g. pressure is meaningless.
> > typical options are:
> > nslist = 0
> > rcoulomb = 0
> > rlist = 0
> > rvdw = 0
> >
> > this means no cut-off, and make a list only once. Very high performace
> > simulations, but scaling as N^2.
>
> Typically only usefulk when you really want a vacuum simulation, i.e. an
> isolated protein without water. I don't think it works well if you use this
> for e.g. a 'protein in a droplet' type of simulation.
>
>
> --
> Groetjes,
>
> Anton
> _____________ _______________________________________________________
> | | |
> | _ _ ___,| K. Anton Feenstra |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
> | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
> | | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
> | | "If You See Me Getting High, Knock Me Down" |
> | | (Red Hot Chili Peppers) |
> |_____________|_______________________________________________________|
>
>
>
> --__--__--
>
> Message: 10
> Date: Mon, 29 Sep 2003 11:23:00 +0200
> From: Lieven Buts <lieven at ultr.vub.ac.be>
> Organization: Vrije Universiteit Brussel (VUB)
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Simple L-J Particles' simulation
> Reply-To: gmx-users at gromacs.org
>
> Anton Feenstra wrote:
> > David wrote:
> > > On Sat, 2003-09-27 at 16:33, Albert Sun wrote:
> > >>Hi, David,
> > >>Thank you for your reply.
> > >>I did as you advised, run grompp once and
> > >> mv mdout.mdp grompp.mdp
> > >>but get " bad comment or file name "
> > >
> > > Oh dear, I hope you're not running windows. Please upgrade to Linux in
> > > that case, otherwise check spelling.
> >
> > The intent of David's command is to change the name of 'mdout.mdp'.
> > By the way, if you look carefully at the messages grompp displays
> > about unknown parameters, you'll find that often also useful hints
> > are given.
>
> The DOS/Windows equivalent of "mv mdout.mdp grompp.mdp" would
> be "ren mdout.mdp grompp.mdp" if I remember correctly.
--
Hernan Alonso <hernan.alonso at anu.edu.au>
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