Hi Nicholas,<br><br>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. <br><br>Thank you<br><br><div class="gmail_quote">On Thu, Dec 3, 2009 at 11:56 AM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br>
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Today's Topics:<br>
<br>
1. Re: Pressure annealing in Gromacs? (Jussi Lehtola)<br>
2. RE: Exclusions in topology file seem not working for big<br>
systems (Berk Hess)<br>
3. "coarse_grain.tcl" script does not show all of the<br>
coarse-grained bonds in vmd (Ozge Engin)<br>
4. Re: "coarse_grain.tcl" script does not show all of the<br>
coarse-grained bonds in vmd (Nicolas Sapay)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 03 Dec 2009 09:22:46 +0200<br>
From: Jussi Lehtola <<a href="mailto:jussi.lehtola@helsinki.fi">jussi.lehtola@helsinki.fi</a>><br>
Subject: Re: [gmx-users] Pressure annealing in Gromacs?<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:1259824966.1913.1.camel@politzer.theorphys.helsinki.fi">1259824966.1913.1.camel@politzer.theorphys.helsinki.fi</a>><br>
Content-Type: text/plain; charset="UTF-8"<br>
<br>
On Thu, 2009-12-03 at 02:30 +1100, Mark Abraham wrote:<br>
> Jussi Lehtola wrote:<br>
> > I'm experiencing trouble converging the density of some heavy liquid<br>
> > alcohols (after 10 ns of simulation the density is still changing<br>
> > linearly). Is there any way to run pressure annealing in Gromacs?<br>
> > Running the system through a high pressure and temperature might give an<br>
> > equilibrium structure quicker.<br>
><br>
> There's nothing native that I'm aware of, but it should be<br>
> straightforward to use sed or perl in a script to do the annealing "by<br>
> hand" in a series of mdrun invocations.<br>
<br>
Yup, that came to mind but then one ends up with N trajectories and log<br>
files. And one has to run a big pile of grompp commands, that waste some<br>
parallel run time, so I really would like something integrated.<br>
<br>
Besides, a thing like changing the reference pressure should be a<br>
no-brainer in the source code - assuming the code is well structured and<br>
one knows it well beforehand.<br>
<br>
Anyway, the problem was solved for now already. Still, pressure<br>
annealing would be a nice addon to gromacs. (I'll open a bug on bugzilla<br>
about it.)<br>
<br>
--<br>
------------------------------------------------------<br>
Jussi Lehtola, FM, Tohtorikoulutettava<br>
Fysiikan laitos, Helsingin Yliopisto<br>
<a href="mailto:jussi.lehtola@helsinki.fi">jussi.lehtola@helsinki.fi</a>, p. 191 50632<br>
------------------------------------------------------<br>
Mr. Jussi Lehtola, M. Sc., Doctoral Student<br>
Department of Physics, University of Helsinki, Finland<br>
<a href="mailto:jussi.lehtola@helsinki.fi">jussi.lehtola@helsinki.fi</a><br>
------------------------------------------------------<br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Thu, 3 Dec 2009 09:30:27 +0100<br>
From: Berk Hess <<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>><br>
Subject: RE: [gmx-users] Exclusions in topology file seem not working<br>
for big systems<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <COL113-W6464FDE0D2532EB97FCA938E940@phx.gbl><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
<br>
Hi,<br>
<br>
If you really had too many exclusions you would get an error message.<br>
<br>
So I just tested this.<br>
I used the couple_moltype option to couple a 389 atom protein.<br>
This generates exclusions between each protein atom and the 388 others.<br>
All interactions are excluded correctly (and re-added as special 1-4's because<br>
of the couple option).<br>
So I don't understand what is going wrong in your case.<br>
<br>
Berk<br>
<br>
Date: Wed, 2 Dec 2009 09:31:03 -0800<br>
From: <a href="mailto:resal81@yahoo.com">resal81@yahoo.com</a><br>
Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<br>
<br>
<br>
Thanks for your response Dr van der Spoel.<br>
<br>
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.<br>
<br>
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:<br>
Can not exclude the lattice Coulomb energy between energy groups<br>
<br>
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.<br>
<br>
Regards,<br>
Reza Salari<br>
<br>
<br>
From: David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>><br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Sent: Wed, December 2, 2009 11:59:49 AM<br>
Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems<br>
<br>
<br>
Reza Salari wrote:<br>
> Hi All,<br>
><br>
> 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).¨<br>
<br>
You can have max 32 exclusions per atom AFAIK.<br>
However you can use energy_group_excluisions in the mdp file.<br>
><br>
> 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<br>
that numbers continue to the last number):<br>
><br>
> [ exclusions]<br>
> 1 2 3 4 5 6 ... 6420<br>
> 2 1 3 4 5 6 ... 6420<br>
> 3 1 2 4 5 6 ... 6420<br>
> ...<br>
> ...<br>
> 6420 1 2 3 ... 6419<br>
><br>
> I used gmxdump to check that the exclusions were actually implemented, and it seems that they were.<br>
><br>
> 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:<br>
><br>
> Coul-SR:Protein-Protein LJ-SR:Protein-Protein Coul-14:Protein-Protein LJ-14:Protein-Protein<br>
> no exclusions -20277.6<br>
-13030.7 37023.9 7890.52<br>
> using exclusions -16221.2 -10332.9 37023.9<br>
7890.52<br>
><br>
><br>
> 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?<br>
><br>
> I appreciate any hint or help.<br>
><br>
> Regards,<br>
> Reza Salari<br>
><br>
<br>
<br>
-- David.<br>
________________________________________________________________________<br>
David van der Spoel, PhD, Professor of Biology<br>
Dept. of Cell and Molecular Biology, Uppsala University.<br>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>
phone: 46 18 471 4205 fax: 46 18 511<br>
755<br>
<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
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<br>
Message: 3<br>
Date: Thu, 3 Dec 2009 11:23:46 +0200<br>
From: Ozge Engin <<a href="mailto:ozge.engin@gmail.com">ozge.engin@gmail.com</a>><br>
Subject: [gmx-users] "coarse_grain.tcl" script does not show all of<br>
the coarse-grained bonds in vmd<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:373874cf0912030123q30e9dd86ve61c8845eec46bd2@mail.gmail.com">373874cf0912030123q30e9dd86ve61c8845eec46bd2@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi all,<br>
<br>
I was trying to show the bonds between my CG beads in VMD. I have four CG<br>
beads per each molecule, and there are 18 separate molecules which contain<br>
these four beads, which results in having 72 CG beads in total. Therefore,<br>
I expect to see 54 CG bonds in the end.<br>
<br>
I used the "coarse_grain.tcl" script to visualize these CG bonds as<br>
suggested on the VMD page. I have two different bead types in the system: CA<br>
and CG. In order to visualize the bonds I used the following command line on<br>
Tk console:<br>
<br>
source coarse_grained.tcl<br>
g_cg -tpr topol.tpr -sel {{name "CA"} {name "CB"}} -rep {Licorice Licorice}<br>
-color {name name}<br>
<br>
After that it gave me the following lines:<br>
<br>
[ g_cg ] Processing "topol.tpr"...<br>
[ g_cg ] Create the bond list for 72 atoms...<br>
[ g_cg ] Rebuild bonds...<br>
[ g_cg ] Create representations...<br>
<br>
which I understood that all the bonds are created successfully, but when I<br>
looked at the screen I could see only one of those CG bonds, but not the<br>
others. Why might be the reason?<br>
<br>
Thanks in advance<br>
--<br>
Ozge Engin<br>
★☆<br>
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Message: 4<br>
Date: Thu, 03 Dec 2009 10:54:28 +0100<br>
From: Nicolas Sapay <<a href="mailto:nicolas.sapay@cermav.cnrs.fr">nicolas.sapay@cermav.cnrs.fr</a>><br>
Subject: Re: [gmx-users] "coarse_grain.tcl" script does not show all<br>
of the coarse-grained bonds in vmd<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4B178AD4.7000501@cermav.cnrs.fr">4B178AD4.7000501@cermav.cnrs.fr</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
<br>
<br>
Ozge Engin a écrit :<br>
> Hi all,<br>
><br>
> I was trying to show the bonds between my CG beads in VMD. I have four<br>
> CG beads per each molecule, and there are 18 separate molecules which<br>
> contain these four beads, which results in having 72 CG beads in<br>
> total. Therefore, I expect to see 54 CG bonds in the end.<br>
><br>
> I used the "coarse_grain.tcl" script to visualize these CG bonds as<br>
> suggested on the VMD page. I have two different bead types in the<br>
> system: CA and CG. In order to visualize the bonds I used the<br>
> following command line on Tk console:<br>
><br>
> source coarse_grained.tcl<br>
> g_cg -tpr topol.tpr -sel {{name "CA"} {name "CB"}} -rep {Licorice<br>
> Licorice} -color {name name}<br>
Hi,<br>
<br>
you mentionned that you have 2 types of beads called CA and CG. Here,<br>
you are selecting beads named CA and CB. Maybe that's where the problem<br>
come from. Try to modify the representations manually (from the<br>
"representation" menu) to see if it change something. If not, that is<br>
probably a bug in the parsing of the gmxdump output. That is where the<br>
bonds come from.<br>
<br>
Cheers,<br>
Nicolas<br>
><br>
> After that it gave me the following lines:<br>
><br>
> [ g_cg ] Processing "topol.tpr"...<br>
> [ g_cg ] Create the bond list for 72 atoms...<br>
> [ g_cg ] Rebuild bonds...<br>
> [ g_cg ] Create representations...<br>
><br>
> which I understood that all the bonds are created successfully, but<br>
> when I looked at the screen I could see only one of those CG bonds,<br>
> but not the others. Why might be the reason?<br>
><br>
> Thanks in advance<br>
> --<br>
> Ozge Engin<br>
> ★☆<br>
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*****************************************<br>
</font></blockquote></div><br><br clear="all"><br>-- <br>Ozge Engin<br> ★☆<br>