[gmx-users] Re: gmx-users Digest, Vol 68, Issue 21
Ozge Engin
ozge.engin at gmail.com
Thu Dec 3 11:30:08 CET 2009
Hi Nicholas,
Sorry, I wrote the bead names wrong in the mail. I have just used the
correct CG names, but could not see any bond other than one.
Thank you
On Thu, Dec 3, 2009 at 11:56 AM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. Re: Pressure annealing in Gromacs? (Jussi Lehtola)
> 2. RE: Exclusions in topology file seem not working for big
> systems (Berk Hess)
> 3. "coarse_grain.tcl" script does not show all of the
> coarse-grained bonds in vmd (Ozge Engin)
> 4. Re: "coarse_grain.tcl" script does not show all of the
> coarse-grained bonds in vmd (Nicolas Sapay)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 03 Dec 2009 09:22:46 +0200
> From: Jussi Lehtola <jussi.lehtola at helsinki.fi>
> Subject: Re: [gmx-users] Pressure annealing in Gromacs?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1259824966.1913.1.camel at politzer.theorphys.helsinki.fi>
> Content-Type: text/plain; charset="UTF-8"
>
> On Thu, 2009-12-03 at 02:30 +1100, Mark Abraham wrote:
> > Jussi Lehtola wrote:
> > > I'm experiencing trouble converging the density of some heavy liquid
> > > alcohols (after 10 ns of simulation the density is still changing
> > > linearly). Is there any way to run pressure annealing in Gromacs?
> > > Running the system through a high pressure and temperature might give
> an
> > > equilibrium structure quicker.
> >
> > There's nothing native that I'm aware of, but it should be
> > straightforward to use sed or perl in a script to do the annealing "by
> > hand" in a series of mdrun invocations.
>
> Yup, that came to mind but then one ends up with N trajectories and log
> files. And one has to run a big pile of grompp commands, that waste some
> parallel run time, so I really would like something integrated.
>
> Besides, a thing like changing the reference pressure should be a
> no-brainer in the source code - assuming the code is well structured and
> one knows it well beforehand.
>
> Anyway, the problem was solved for now already. Still, pressure
> annealing would be a nice addon to gromacs. (I'll open a bug on bugzilla
> about it.)
>
> --
> ------------------------------------------------------
> Jussi Lehtola, FM, Tohtorikoulutettava
> Fysiikan laitos, Helsingin Yliopisto
> jussi.lehtola at helsinki.fi, p. 191 50632
> ------------------------------------------------------
> Mr. Jussi Lehtola, M. Sc., Doctoral Student
> Department of Physics, University of Helsinki, Finland
> jussi.lehtola at helsinki.fi
> ------------------------------------------------------
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 3 Dec 2009 09:30:27 +0100
> From: Berk Hess <gmx3 at hotmail.com>
> Subject: RE: [gmx-users] Exclusions in topology file seem not working
> for big systems
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <COL113-W6464FDE0D2532EB97FCA938E940 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Hi,
>
> If you really had too many exclusions you would get an error message.
>
> So I just tested this.
> I used the couple_moltype option to couple a 389 atom protein.
> This generates exclusions between each protein atom and the 388 others.
> All interactions are excluded correctly (and re-added as special 1-4's
> because
> of the couple option).
> So I don't understand what is going wrong in your case.
>
> Berk
>
> Date: Wed, 2 Dec 2009 09:31:03 -0800
> From: resal81 at yahoo.com
> Subject: Re: [gmx-users] Exclusions in topology file seem not working for
> big systems
> To: gmx-users at gromacs.org
>
>
>
> Thanks for your response Dr van der Spoel.
>
> Then there is a limit on the number of atoms that can be defined in the
> exclusions section. My smaller system has 60 atoms and I used exclusions
> successfully for that, so I guess the limit might be a little more than 32.
>
> Regarding the use of energygrp_excl,it seems it does not work with PME. If
> I define the protein in the energygrp_excl group, grompp gives me this
> warning:
> Can not exclude the lattice Coulomb energy between energy groups
>
> Which I think means some of electrostatics is not going to be excluded
> between protein atoms. Is there a workaround for this? I think my last
> resort would be to run a simulation first with PME and without exclusions,
> and then rerunning it but this time by defining protein in the
> energygrp_excl and using cut-off instead of PME. Then I guess I will be
> left with only protein-water interactions.
>
> Regards,
> Reza Salari
>
>
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Wed, December 2, 2009 11:59:49 AM
> Subject: Re: [gmx-users] Exclusions in topology file seem not working for
> big systems
>
>
> Reza Salari wrote:
> > Hi All,
> >
> > I seem to have a hard time to use exclusions in topology file. I have a
> relatively big system (~400 aa) that I am trying to calculate the difference
> in desolvation energy (dA) upon turning off charges on a specific residue
> using thermodynamics integration method. The system is a complex of two
> proteins and is frozen inside the box (for my project I need it to be
> frozen).¨
>
> You can have max 32 exclusions per atom AFAIK.
> However you can use energy_group_excluisions in the mdp file.
> >
> > To calculate the desolvation energy, I need to exclude all the
> non-bonding interactions among protein atoms, then the dA that I get
> corresponds to the desolvation energy (and doesn't include the lost
> interactions between mutated residue and the rest of protein). I couldn't
> use energygrp_excl in mdp file since I am using PME. So I defined
> exclusions in topology file as follows (three-dot means
> that numbers continue to the last number):
> >
> > [ exclusions]
> > 1 2 3 4 5 6 ... 6420
> > 2 1 3 4 5 6 ... 6420
> > 3 1 2 4 5 6 ... 6420
> > ...
> > ...
> > 6420 1 2 3 ... 6419
> >
> > I used gmxdump to check that the exclusions were actually implemented,
> and it seems that they were.
> >
> > However when I use g_energy, I don't get zero energy for short range
> interactions. Here are the results of g_energy for simulations with and
> without exclusions:
> >
> > Coul-SR:Protein-Protein LJ-SR:Protein-Protein
> Coul-14:Protein-Protein LJ-14:Protein-Protein
> > no exclusions -20277.6
> -13030.7 37023.9
> 7890.52
> > using exclusions -16221.2
> -10332.9
> 37023.9
> 7890.52
> >
> >
> > I did the same test with a small system (~6 residue) and I did get zero
> SR interactions. While the exclusions work for my small system, I don't know
> why they seem not working for my bigger system. Am I missing something here
> or is there something like an implicit limit for the number of atoms that
> can be defined in the exclusion section of topology file?
> >
> > I appreciate any hint or help.
> >
> > Regards,
> > Reza Salari
> >
>
>
> -- David.
> ________________________________________________________________________
> David van der Spoel, PhD, Professor of Biology
> 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://folding.bmc.uu.se
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>
> Message: 3
> Date: Thu, 3 Dec 2009 11:23:46 +0200
> From: Ozge Engin <ozge.engin at gmail.com>
> Subject: [gmx-users] "coarse_grain.tcl" script does not show all of
> the coarse-grained bonds in vmd
> To: gmx-users at gromacs.org
> Message-ID:
> <373874cf0912030123q30e9dd86ve61c8845eec46bd2 at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi all,
>
> I was trying to show the bonds between my CG beads in VMD. I have four CG
> beads per each molecule, and there are 18 separate molecules which contain
> these four beads, which results in having 72 CG beads in total. Therefore,
> I expect to see 54 CG bonds in the end.
>
> I used the "coarse_grain.tcl" script to visualize these CG bonds as
> suggested on the VMD page. I have two different bead types in the system:
> CA
> and CG. In order to visualize the bonds I used the following command line
> on
> Tk console:
>
> source coarse_grained.tcl
> g_cg -tpr topol.tpr -sel {{name "CA"} {name "CB"}} -rep {Licorice Licorice}
> -color {name name}
>
> After that it gave me the following lines:
>
> [ g_cg ] Processing "topol.tpr"...
> [ g_cg ] Create the bond list for 72 atoms...
> [ g_cg ] Rebuild bonds...
> [ g_cg ] Create representations...
>
> which I understood that all the bonds are created successfully, but when I
> looked at the screen I could see only one of those CG bonds, but not the
> others. Why might be the reason?
>
> Thanks in advance
> --
> Ozge Engin
> ★☆
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> ------------------------------
>
> Message: 4
> Date: Thu, 03 Dec 2009 10:54:28 +0100
> From: Nicolas Sapay <nicolas.sapay at cermav.cnrs.fr>
> Subject: Re: [gmx-users] "coarse_grain.tcl" script does not show all
> of the coarse-grained bonds in vmd
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4B178AD4.7000501 at cermav.cnrs.fr>
> Content-Type: text/plain; charset="utf-8"
>
>
>
> Ozge Engin a écrit :
> > Hi all,
> >
> > I was trying to show the bonds between my CG beads in VMD. I have four
> > CG beads per each molecule, and there are 18 separate molecules which
> > contain these four beads, which results in having 72 CG beads in
> > total. Therefore, I expect to see 54 CG bonds in the end.
> >
> > I used the "coarse_grain.tcl" script to visualize these CG bonds as
> > suggested on the VMD page. I have two different bead types in the
> > system: CA and CG. In order to visualize the bonds I used the
> > following command line on Tk console:
> >
> > source coarse_grained.tcl
> > g_cg -tpr topol.tpr -sel {{name "CA"} {name "CB"}} -rep {Licorice
> > Licorice} -color {name name}
> Hi,
>
> you mentionned that you have 2 types of beads called CA and CG. Here,
> you are selecting beads named CA and CB. Maybe that's where the problem
> come from. Try to modify the representations manually (from the
> "representation" menu) to see if it change something. If not, that is
> probably a bug in the parsing of the gmxdump output. That is where the
> bonds come from.
>
> Cheers,
> Nicolas
> >
> > After that it gave me the following lines:
> >
> > [ g_cg ] Processing "topol.tpr"...
> > [ g_cg ] Create the bond list for 72 atoms...
> > [ g_cg ] Rebuild bonds...
> > [ g_cg ] Create representations...
> >
> > which I understood that all the bonds are created successfully, but
> > when I looked at the screen I could see only one of those CG bonds,
> > but not the others. Why might be the reason?
> >
> > Thanks in advance
> > --
> > Ozge Engin
> > ★☆
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> End of gmx-users Digest, Vol 68, Issue 21
> *****************************************
>
--
Ozge Engin
★☆
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