Re: [gmx-users] gromacs invsqrt() overlaps with icc invsqrt()
wing procedure:
#
#!/bin/bash
for i in `find ./gromacs-4.0.4`; do
sed 's/invsqrt/invSAFEsqrt/g' $i tmp;
mv tmp $i;
done
chmod +x ./gromacs-4.0.4/configure
Using sed -i is a bit more elegant and keeps the permissions, IIRC.
Correct. You can also drop the for loop and do:
sed -i s/invsqrt/invSAFEsqrt/g `find ./gromacs-4.0.4`
or even
find ./gromacs-4.0.4 -type f -exec sed -i s/invsqrt/invSAFEsqrt/g {};
Cheers,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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[gmx-users] lincs warning
Dears, I am experiencing some problems running a few proteins in water (GROMOS43a1/SPC) with gmx-4.0.4 using 32 CPUs. After some ns lincs warnings appear and eventually the simulation crashes dues to too many lincs warnings. When restarting the simulation feeding -cpi md.cpt to mdrun the simulation restarts fine and no lincs warning are reported on the same portion of the simulation. The simulation runs again for some ns and the same happens: new lincs warning appear and eventually the simulation crashes again. Any explanation for this? Any solution? Best, XAvier. ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] lincs warning
XAvier Periole wrote: Dears, I am experiencing some problems running a few proteins in water (GROMOS43a1/SPC) with gmx-4.0.4 using 32 CPUs. After some ns lincs warnings appear and eventually the simulation crashes dues to too many lincs warnings. When restarting the simulation feeding -cpi md.cpt to mdrun the simulation restarts fine and no lincs warning are reported on the same portion of the simulation. The simulation runs again for some ns and the same happens: new lincs warning appear and eventually the simulation crashes again. Any explanation for this? Any solution? Check out 4.0.5 release notes? Check out 4.0.5? Mark ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Resizing heterogeneous membrane (POPG/POPE mixture)
By some fluke one of the layers consists of the lipid ratio I require (while the other does not). I will try your suggestion regarding to horizontal flip of that layer. Thanks! -Shay -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Tuesday, June 02, 2009 23:49 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Resizing heterogeneous membrane (POPG/POPE mixture) Shay Amram wrote: Dear GROMACS users, I have been trying to expand a membrane by a non-integer multiplier (for example X1.5). This can be done using *genbox -cs Membrane.gro -o Expanded_membrane.gro -box 1.5X 1.5Y Z*** This has worked very good with _homogenous_ membranes, and only very short equilibrium times were required to re-equilibrate the membrane (~10-20ns). Now I am trying to deal the same way with _heterogeneous_ membrane (POPG/POPE mixture, Mikko Karttunen et. al). When trying to invoke the above command to the POPG/POPE membrane I get a membrane with different compositions of lipids in the upper and lower leaflets. This happens (so I suspect) because the arrangement of lipids in each leaflet is somewhat different so that the molecules that get' to be multiplied do not conserve the same ratio of different lipids as in the original structure (which has ratio of 1:3 POPG/POPE). If you have an excess of POPE, you can (either manually, or by using a script) randomly choose some POPE to be converted to (or replaced with) POPG by some clever means. This is not a trivial task. Is there a way to multiply the membrane by a _non-integer_ number AND somehow conserve the ratio of different lipid species too? The output is dependent upon the configuration of the input and the box size, so no, there is no straightforward, automatic, way of doing so given the constraints of your box dimensions. Or at the very least, to have both upper and lower leaflets identical after multiplication? (This, too, would help immensely). If you can construct a satisfactory monolayer, you can manipulate its coordinates (i.e. horizontal flip and translation) to create a bilayer. You would have to do plenty of equilibration after doing so, of course. -Justin Thanks, -Shay ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fwd: problem with FES4 cluster
Subarna, I am not a helpdesk or mailing list, if I had had the answer, I would have replied on the mailing list already. Then, if you feel it is appropriate to send a mail to someone you don't know, at least take the effort to write a complete message. Tsjerk -- Forwarded message -- From: subarna thakur thakur.suba...@yahoo.co.in Date: Wed, Jun 3, 2009 at 9:34 AM Subject: problem with FES4 cluster To: tsje...@gmail.com Hi I am facing a problem with a protein with Ferro sulphur cluster (FS4),I am unable to construct the .gro file with pdb2gmx command. How do i construct the topology file of the ligand and where do I add the appropriate definitions for the bonds, angles, dihedrals, pairs, etc. Subarna Thkaur Ph.D Student University of North Bengal Cricket on your mind? Visit the ultimate cricket website. Enter now! -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] lincs warning
On Jun 3, 2009, at 9:51 AM, Mark Abraham wrote: XAvier Periole wrote: Dears, I am experiencing some problems running a few proteins in water (GROMOS43a1/SPC) with gmx-4.0.4 using 32 CPUs. After some ns lincs warnings appear and eventually the simulation crashes dues to too many lincs warnings. When restarting the simulation feeding -cpi md.cpt to mdrun the simulation restarts fine and no lincs warning are reported on the same portion of the simulation. The simulation runs again for some ns and the same happens: new lincs warning appear and eventually the simulation crashes again. Any explanation for this? Any solution? Check out 4.0.5 release notes? Check out 4.0.5? Yes. Nothing that seem to matter to these lincs warnings! Mark ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] lincs warning
Hi XAvier, Do you use virtual sites? I've seen this when I used virtual sites, large time steps and a system that probably wasn't equilibrated enough. Ran. XAvier Periole wrote: Dears, I am experiencing some problems running a few proteins in water (GROMOS43a1/SPC) with gmx-4.0.4 using 32 CPUs. After some ns lincs warnings appear and eventually the simulation crashes dues to too many lincs warnings. When restarting the simulation feeding -cpi md.cpt to mdrun the simulation restarts fine and no lincs warning are reported on the same portion of the simulation. The simulation runs again for some ns and the same happens: new lincs warning appear and eventually the simulation crashes again. Any explanation for this? Any solution? Best, XAvier. ___ gmx-users mailing listgmx-users@gromacs.org 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] lincs warning
On Jun 3, 2009, at 10:01 AM, Ran Friedman wrote: Hi XAvier, Do you use virtual sites? I've seen this when I used virtual sites, No virtual sites. large time steps and a system that probably wasn't equilibrated enough. time step 2 fs and a system totally equilibrated, nothing there. I would have considered this if the warning were reproduced when restarting the simulation. It seems more that it is a loss of accuracy due to communication between CPUs ? XAvier. Ran. XAvier Periole wrote: Dears, I am experiencing some problems running a few proteins in water (GROMOS43a1/SPC) with gmx-4.0.4 using 32 CPUs. After some ns lincs warnings appear and eventually the simulation crashes dues to too many lincs warnings. When restarting the simulation feeding -cpi md.cpt to mdrun the simulation restarts fine and no lincs warning are reported on the same portion of the simulation. The simulation runs again for some ns and the same happens: new lincs warning appear and eventually the simulation crashes again. Any explanation for this? Any solution? Best, XAvier. ___ gmx-users mailing listgmx-users@gromacs.org 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] .itp file for an electrode
Hello everbody I'm trying to repeat a simulation which is reported in a paper. I'm going to model an electrode according to this exact method reported in this paper the electrodes were modeled as two parallel XY square lattices made of charged Lennard-Jones spheres with radii 0.11 nm. Surface charge densities on the electrodes were varied by the partial charge of the lattice spheres. I'm looking for the .itp file for a metalic electrode. Does anyone by any chance have such a file? Thank you all so much -- Negar Ashari Astani ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] .itp file for an electrode
It is not very difficult to construct a topology (itp-file) for one atom. You may look at the definitions of sodium or chloride in the .rtp file for the force field you want to use and adapt them to your needs. Then you need the atom coordinates of the two parallel lattices, which you can make with genconf starting from a one atom coordinate file. Andreas --- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Negar Ashari Astani Sent: 03 June 2009 09:22 To: gmx-users@gromacs.org Subject: [gmx-users] .itp file for an electrode Hello everbody I'm trying to repeat a simulation which is reported in a paper. I'm going to model an electrode according to this exact method reported in this paper the electrodes were modeled as two parallel XY square lattices made of charged Lennard-Jones spheres with radii 0.11 nm. Surface charge densities on the electrodes were varied by the partial charge of the lattice spheres. I'm looking for the .itp file for a metalic electrode. Does anyone by any chance have such a file? Thank you all so much -- Negar Ashari Astani ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with FeS cluster
Hello user Can anybody please tell me how to prepare a topology file for the FES4 cluster incorporated in a protein Subarna Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] lincs warning
XAvier Periole skrev: On Jun 3, 2009, at 10:01 AM, Ran Friedman wrote: Hi XAvier, Do you use virtual sites? I've seen this when I used virtual sites, No virtual sites. large time steps and a system that probably wasn't equilibrated enough. time step 2 fs and a system totally equilibrated, nothing there. I would have considered this if the warning were reproduced when restarting the simulation. It seems more that it is a loss of accuracy due to communication between CPUs ? If you use dynamic load balancing then you are sacrificing binary reproducibility. Because of this, and the chaotic nature of MD, the error will likely not occur at the same point in your continuation. Still, the source of the error persists and is what demands attention I'd say. XAvier. Ran. XAvier Periole wrote: Dears, I am experiencing some problems running a few proteins in water (GROMOS43a1/SPC) with gmx-4.0.4 using 32 CPUs. After some ns lincs warnings appear and eventually the simulation crashes dues to too many lincs warnings. When restarting the simulation feeding -cpi md.cpt to mdrun the simulation restarts fine and no lincs warning are reported on the same portion of the simulation. The simulation runs again for some ns and the same happens: new lincs warning appear and eventually the simulation crashes again. Any explanation for this? Any solution? Best, XAvier. ___ gmx-users mailing listgmx-users@gromacs.org 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_dist: extract distances between any two atom pairs
Dear Gromacs Users, I need to extract all possible distances between any two atom pairs of a small hexa- to dodecamer from a trajectory. The same is necessary for all dihedral angles of this protein. Now I wonder if this is possible without defining all of them manually in the ndx file and call g_dist for each of them ? Is there a short answer on that ? Maybe I missed the answer to that question in the forum ?! greetings, joern ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] lincs warning
On Jun 3, 2009, at 10:58 AM, Giovanni Bussi wrote: Dear Xavier, With the default flag for pbc (periodic_molecules=no) you may end up in lincs problem if an atom of the protein becomes too close to the image of another atom of the protein. If this is your case, use periodic_molecules=yes, or enlarge the solvation cell. Thanks, I have however a very large water box and no problem there I believe. Hope this helps, Giovanni On Wed, Jun 3, 2009 at 10:48 AM, Erik Marklund er...@xray.bmc.uu.se wrote: XAvier Periole skrev: On Jun 3, 2009, at 10:01 AM, Ran Friedman wrote: Hi XAvier, Do you use virtual sites? I've seen this when I used virtual sites, No virtual sites. large time steps and a system that probably wasn't equilibrated enough. time step 2 fs and a system totally equilibrated, nothing there. I would have considered this if the warning were reproduced when restarting the simulation. It seems more that it is a loss of accuracy due to communication between CPUs ? If you use dynamic load balancing then you are sacrificing binary reproducibility. Because of this, and the chaotic nature of MD, the error will likely not occur at the same point in your continuation. Still, the source of the error persists and is what demands attention I'd say. XAvier. Ran. XAvier Periole wrote: Dears, I am experiencing some problems running a few proteins in water (GROMOS43a1/SPC) with gmx-4.0.4 using 32 CPUs. After some ns lincs warnings appear and eventually the simulation crashes dues to too many lincs warnings. When restarting the simulation feeding -cpi md.cpt to mdrun the simulation restarts fine and no lincs warning are reported on the same portion of the simulation. The simulation runs again for some ns and the same happens: new lincs warning appear and eventually the simulation crashes again. Any explanation for this? Any solution? Best, XAvier. ___ gmx-users mailing listgmx-users@gromacs.org 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] lincs warning
On Jun 3, 2009, at 10:48 AM, Erik Marklund wrote: XAvier Periole skrev: On Jun 3, 2009, at 10:01 AM, Ran Friedman wrote: Hi XAvier, Do you use virtual sites? I've seen this when I used virtual sites, No virtual sites. large time steps and a system that probably wasn't equilibrated enough. time step 2 fs and a system totally equilibrated, nothing there. I would have considered this if the warning were reproduced when restarting the simulation. It seems more that it is a loss of accuracy due to communication between CPUs ? If you use dynamic load balancing then you are sacrificing binary reproducibility. Because of this, and the chaotic nature of MD, the error will likely not occur at the same point in your continuation. Still, the source of the error persists and is what demands attention I'd say. Well starting from a cpt file, I would expect reproducibility at the difference that the decomposition over CPUs might be refreshed. It might be but I am still favoring a communication issue. I am now testing the effect of using -rdd and -rcon on the LINCS warnings. XAvier. Ran. XAvier Periole wrote: Dears, I am experiencing some problems running a few proteins in water (GROMOS43a1/SPC) with gmx-4.0.4 using 32 CPUs. After some ns lincs warnings appear and eventually the simulation crashes dues to too many lincs warnings. When restarting the simulation feeding -cpi md.cpt to mdrun the simulation restarts fine and no lincs warning are reported on the same portion of the simulation. The simulation runs again for some ns and the same happens: new lincs warning appear and eventually the simulation crashes again. Any explanation for this? Any solution? Best, XAvier. ___ gmx-users mailing listgmx-users@gromacs.org 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem in inflategro
Samik Bhattacharya wrote: hi i am simulating a membrane protein where i am facing some difficulties in running the inflategro.pl available at http://moose.bio.ucalgary.ca. i cant understand what should be the input of areaperlipid.dat file? where can i find that file ? or i've to make it myself? also contents of the same file is not very claer to me... pls a little help will be very encouraging. Thanking you The areaperlipid.dat is output, a way of assessing progress of the inflating/shrinking process. -Justin Shamik Explore and discover exciting holidays and getaways with Yahoo! India Travel Click here! http://in.rd.yahoo.com/tagline_Travel_1/*http://in.travel.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with FeS cluster
subarna thakur wrote: Hello user Can anybody please tell me how to prepare a topology file for the FES4 cluster incorporated in a protein I passed along some useful information to you yesterday. There is no easy answer. To do so would involve a large amount of work, in any case, if it is even possible to model this species using a standard MM force field. -Justin Subarna Cricket on your mind? Visit the ultimate cricket website. Enter now! http://in.rd.yahoo.com/tagline_cricket_1/*http://beta.cricket.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_dist: extract distances between any two atom pairs
Joern Lenz wrote: Dear Gromacs Users, I need to extract all possible distances between any two atom pairs of a small hexa- to dodecamer from a trajectory. The same is necessary for all dihedral angles of this protein. Now I wonder if this is possible without defining all of them manually in the ndx file and call g_dist for each of them ? Is there a short answer on that ? Maybe I missed the answer to that question in the forum ?! That level of detail might just require some iterative calls to g_dist and g_angle, unfortunately. Scripts are your friend, here. Also, g_mdmat might be useful, but it plots minimum distances between *residue* pairs, not atom pairs. Much more convenient than repeated calls to g_dist, however :) -Justin greetings, joern ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with FeS cluster
Hi I have gone through the material you have earlier mentioned but I am still in dark and not sure where to start. Should I make chages in the relevent .rtp file to incorporate the atoms of the FE-S cluster? Subarna From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-us...@gromacs..org Sent: Wednesday, 3 June, 2009 4:46:37 PM Subject: Re: [gmx-users] problem with FeS cluster subarna thakur wrote: Hello user Can anybody please tell me how to prepare a topology file for the FES4 cluster incorporated in a protein I passed along some useful information to you yesterday. There is no easy answer. To do so would involve a large amount of work, in any case, if it is even possible to model this species using a standard MM force field. -Justin Subarna Cricket on your mind? Visit the ultimate cricket website. Enter now! http://in.rd.yahoo.com/tagline_cricket_1/*http://beta.cricket.yahoo..com ___ gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Own a website.Get an unlimited package.Pay next to nothing.*Go to http://in.business.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Normal of the benzene and z axis.
Thanks for the reply. But I have tried use g_sorient tool and I could not see what the sequence of index give me a normal vector of the molecule of benzene. There another tool for this analysis? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br On Tue, Jun 2, 2009 at 9:01 AM, Eudes Fileti fil...@ufabc.edu.br wrote: Dear gmx users;How can I calculate the angle distribution forthe angle between the normal of the benzene and z axis? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Normal of the benzene and z axis.
Eudes Fileti wrote: Thanks for the reply. But I have tried use g_sorient tool and I could not see what the sequence of index give me a normal vector of the molecule of benzene. three carbons in the ring. There another tool for this analysis? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br On Tue, Jun 2, 2009 at 9:01 AM, Eudes Fileti fil...@ufabc.edu.br mailto:fil...@ufabc.edu.br wrote: Dear gmx users; How can I calculate the angle distribution for the angle between the normal of the benzene and z axis? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Re: Normal of the benzene and z axis.
Dear David, thanks for the reply. In fact 3 carbons can provide me the normal vector of the molecule. But according to manual, g_sorient considers the angle formed by the triple 1 2 3, as the vector that goes from 2 to the midpoint of 1 and 3 (which is the plan of the molecule). So how can I to build a index file for g_sorient to plot the normal vector? Sorry if the question is obvious and I can't to see. Bests ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 Message: 5 Date: Wed, 3 Jun 2009 09:08:43 -0300 From: Eudes Fileti fil...@ufabc.edu.br Subject: [gmx-users] Re: Normal of the benzene and z axis. To: gmx-users@gromacs.org Message-ID: 65e289a20906030508y708e2633rddba6dc6c8f16...@mail.gmail.com Content-Type: text/plain; charset=windows-1252 Thanks for the reply. But I have tried use g_sorient tool and I could not see what the sequence of index give me a normal vector of the molecule of benzene. There another tool for this analysis? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br On Tue, Jun 2, 2009 at 9:01 AM, Eudes Fileti fil...@ufabc.edu.br wrote: Dear gmx users;How can I calculate the angle distribution forthe angle between the normal of the benzene and z axis? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090603/31b76231/attachment-0001.html -- Eudes Fileti wrote: Thanks for the reply. But I have tried use g_sorient tool and I could not see what the sequence of index give me a normal vector of the molecule of benzene. three carbons in the ring. There another tool for this analysis? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br On Tue, Jun 2, 2009 at 9:01 AM, Eudes Fileti fil...@ufabc.edu.br mailto:fil...@ufabc.edu.br wrote: Dear gmx users; How can I calculate the angle distribution for the angle between the normal of the benzene and z axis? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Resizing heterogeneous membrane (POPG/POPE mixture)
Shay Amram a écrit : Dear GROMACS users, I have been trying to expand a membrane by a non-integer multiplier (for example X1.5). This can be done using *genbox -cs Membrane.gro -o Expanded_membrane.gro –box 1.5X 1.5Y Z*** This has worked very good with _homogenous_ membranes, and only very short equilibrium times were required to re-equilibrate the membrane (~10-20ns). Now I am trying to deal the same way with _heterogeneous_ membrane (POPG/POPE mixture, Mikko Karttunen et. al). When trying to invoke the above command to the POPG/POPE membrane I get a membrane with different compositions of lipids in the upper and lower leaflets. This happens (so I suspect) because the arrangement of lipids in each leaflet is somewhat different so that the molecules that get' to be multiplied do not conserve the same ratio of different lipids as in the original structure (which has ratio of 1:3 POPG/POPE). Is there a way to multiply the membrane by a _non-integer_ number AND somehow conserve the ratio of different lipid species too? Or at the very least, to have both upper and lower leaflets identical after multiplication? (This, too, would help immensely). This is quite a difficult task unfortunately. Personally, I create a membrane patch larger than the one I want (e.g. 2x 2y 1z), load the gro file into VMD, then cut a patch the size/composition I need. That means doing selections like: set sel [atomselect top same resid as (x... and x... and y... and y...)] Checking the number of lipids in each layer: [atomselect top resname DOPG and name P1 and z... and (same resid as (x... and x... and y... and y...))] num [atomselect top resname DOPG and name P1 and z... and (same resid as (x... and x... and y... and y...))] num Completing the selection by manually adding the residues I need: set sel [atomselect top same resid as (x... and x... and y... and y...) or resid ...] Saving the coordinates: animate write pdb sel $sel This is a tidy task and some equilibration is still required after that. Basic knowledge of TCL/VMD scripting languages may be required to facilitate/automate the work. Nicolas Thanks, -Shay ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php begin:vcard fn:Nicolas Sapay n:Sapay;Nicolas org:CERMAV;Molecular Glycobiology adr;quoted-printable:601 rue de la Chimie ;;Domaine Universitaire;Saint Martin d'H=C3=A8res;;38400;France email;internet:nicolas.sa...@cermav.cnrs.fr title:Post-Doctoral Fellow tel;work:+33 [0]4 76 03 76 44 tel;fax:+33 [0]4 76 54 72 03 x-mozilla-html:FALSE url:http://www.cermav.cnrs.fr/ version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Re: Normal of the benzene and z axis.
Eudes Fileti wrote: Dear David, thanks for the reply. In fact 3 carbons can provide me the normal vector of the molecule. But according to manual, g_sorient considers the angle formed by the triple 1 2 3, as the vector that goes from 2 to the midpoint of 1 and 3 (which is the plan of the molecule). So how can I to build a index file for g_sorient to plot the normal vector? g_sorient -h: g_sorient analyzes solvent orientation around solutes. It calculates two angles between the vector from one or more reference positions to the first atom of each solvent molecule: theta1: the angle with the vector from the first atom of the solvent molecule to the midpoint between atoms 2 and 3. theta2: the angle with the normal of the solvent plane, defined by the same three atoms, or when the option -v23 is set the angle with the vector between atoms 2 and 3. The reference can be a set of atoms or the center of mass of a set of atoms. The group of solvent atoms should consist of 3 atoms per solvent molecule. Only solvent molecules between -rmin and -rmax are considered for -o and -no each frame. Sorry if the question is obvious and I can't to see. Bests ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 Message: 5 Date: Wed, 3 Jun 2009 09:08:43 -0300 From: Eudes Fileti fil...@ufabc.edu.br mailto:fil...@ufabc.edu.br Subject: [gmx-users] Re: Normal of the benzene and z axis. To: gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 65e289a20906030508y708e2633rddba6dc6c8f16...@mail.gmail.com mailto:65e289a20906030508y708e2633rddba6dc6c8f16...@mail.gmail.com Content-Type: text/plain; charset=windows-1252 Thanks for the reply. But I have tried use g_sorient tool and I could not see what the sequence of index give me a normal vector of the molecule of benzene. There another tool for this analysis? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br On Tue, Jun 2, 2009 at 9:01 AM, Eudes Fileti fil...@ufabc.edu.br mailto:fil...@ufabc.edu.br wrote: Dear gmx users;How can I calculate the angle distribution forthe angle between the normal of the benzene and z axis? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090603/31b76231/attachment-0001.html -- Eudes Fileti wrote: Thanks for the reply. But I have tried use g_sorient tool and I could not see what the sequence of index give me a normal vector of the molecule of benzene. three carbons in the ring. There another tool for this analysis? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br On Tue, Jun 2, 2009 at 9:01 AM, Eudes Fileti fil...@ufabc.edu.br mailto:fil...@ufabc.edu.br mailto:fil...@ufabc.edu.br mailto:fil...@ufabc.edu.br wrote: Dear gmx users; How can I calculate the angle distribution for the angle between the normal of the benzene and z axis? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David
Re: [gmx-users] problem with FeS cluster
subarna thakur wrote: Hi I have gone through the material you have earlier mentioned but I am still in dark and not sure where to start. Should I make chages in the relevent .rtp file to incorporate the atoms of the FE-S cluster? If you derive your own parameters, you can either make an .rtp entry for the cluster, or simply generate an .itp file by hand. Either way will work, but no matter what, it is not a trivial task to derive the appropriate parameters. Making and .rtp entry/.itp file is simple, proving the validity of your parameters is not. -Justin Subarna *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wednesday, 3 June, 2009 4:46:37 PM *Subject:* Re: [gmx-users] problem with FeS cluster subarna thakur wrote: Hello user Can anybody please tell me how to prepare a topology file for the FES4 cluster incorporated in a protein I passed along some useful information to you yesterday. There is no easy answer. To do so would involve a large amount of work, in any case, if it is even possible to model this species using a standard MM force field. -Justin Subarna Cricket on your mind? Visit the ultimate cricket website. Enter now! http://in.rd.yahoo.com/tagline_cricket_1/*http://beta.cricket.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Bollywood news, movie reviews, film trailers and more! Click here. http://in.rd.yahoo.com/tagline_movies_1/*http://in.movies.yahoo.com/?wm=n/ -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] protein running out of box
Hello, every body. I have running a MD for 10ns. However, after 5ns part of protein will running out of the box and be located at other part of the water box. And the whole structure seems ver strange. It seems that it was caused by the mass translation but I have used the comm_mode=Linear. Any suggestions? -- Zhen Chen, Department of Bioprocess and Biosystem Engineering, Hamburg University of Technology, Denickestr. 15, D-21071, Hamburg,Germany Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: zhen.c...@tuhh.de ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] protein running out of box
sheerychen wrote: Hello, every body. I have running a MD for 10ns. However, after 5ns part of protein will running out of the box and be located at other part of the water box. And the whole structure seems ver strange. It seems that it was caused by the mass translation but I have used the comm_mode=Linear. Any suggestions? What you are seeing is a normal consequence of periodicity. There is no side in an infinite system: http://oldwiki.gromacs.org/index.php/Periodic_Boundary_Conditions -Justin -- Zhen Chen, Department of Bioprocess and Biosystem Engineering, Hamburg University of Technology, Denickestr. 15, D-21071, Hamburg,Germany Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: zhen.c...@tuhh.de mailto:zhen.c...@tuhh.de ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] protein running out of box
Dear Zhen Chen Protein is located stranger(sometime at the one side of the protein,in other frame other side). Its not a problem. Your simulation is fine. it is due to you had given PBC. thats why. You can reset your trejectory using trjconv. regards Ravi Datta Sharma Lecturer, Bioinformatics, Department of Microbiology, CCS Unversity, Meerut --- On Wed, 3/6/09, sheerychen sheeryc...@gmail.com wrote: From: sheerychen sheeryc...@gmail.com Subject: [gmx-users] protein running out of box To: gmx-users@gromacs.org Date: Wednesday, 3 June, 2009, 7:07 PM Hello, every body. I have running a MD for 10ns. However, after 5ns part of protein will running out of the box and be located at other part of the water box. And the whole structure seems ver strange. It seems that it was caused by the mass translation but I have used the comm_mode=Linear. Any suggestions? -- Zhen Chen, Department of Bioprocess and Biosystem Engineering, Hamburg University of Technology, Denickestr. 15, D-21071, Hamburg,Germany Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: zhen.c...@tuhh.de -Inline Attachment Follows- ___ gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Own a website.Get an unlimited package.Pay next to nothing.*Go to http://in.business.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] spc.itp for the amber force field
Hi, I am trying to simulate a system using the parameters for ions developed by Joung et al. and implemented in Amber (frcmod.ionsjc_spce). I have the topology and the crd file. Now, I want to obtain the topology for Gromacs using amb2gmx.pl, so I must change the default parameters (for tip3p) included in amb2gmx.pl. I have seen that in the .tar file ffamber_v4.0 there is no a corresponding itp file for spc model of water in amber, so what parameters should I include for the section of bondtypes, angletypes, atoms, bonds, angles, settles,...? Those corresponding to the SCP in Gromacs directly? Thank you very much for your help. Best wishes, Rebeca Garcia Academic Visitor Oxford University _ Chatea sin límites en Messenger con la tarifa plana de Orange http://serviciosmoviles.es.msn.com/messenger/orange.aspx___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Some questions regarding generating topologies
Hi, Even though after going through the manual, I still have some basic confusions regarding generating topologies. 1) I have generated an itp file after adding some Cl- ions using genion. It goes like this: [ moleculetype ] ; Namenrexcl Cl_ion 0 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1CL- 1Cl- Cl 1 -1 35.453 ; qtot -1 2CL- 2Cl- Cl 2 -1 35.453 ; qtot -2 3CL- 3Cl- Cl 3 -1 35.453 ; qtot -3 To allow nb interactions between all the atoms in the molecule Cl_ion, is setting nrexcl = 0 okay? 2) In spce.itp provided with GROMACS, [ moleculetype ] ; molname nrexcl SOL 2 while in the manual, on pg. 100 (Chapter-5 Topologies) [ moleculetype ] ; molname nrexcl SOL 1 why is the inconsistency? 3) I am using SPC/E water model with GROMOS96 43a1 ff, (SPC is recommended). Since SPC/E is one of the most used model, should I consider using OPLS rather than GROMOS96, otherwise how significant will be the errors? 4) I am using GROMOS96 43a1, so am I allowed to change combination rule to '2' ( '1' is the default). How significantly will it affect the simulations? Any relevant idea/suggestion/reference is appreciated. Thanks, Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Some questions regarding generating topologies
On Wed, Jun 3, 2009 at 9:04 PM, Justin A. Lemkul jalem...@vt.edu wrote: Manik Mayur wrote: Hi, Even though after going through the manual, I still have some basic confusions regarding generating topologies. 1) I have generated an itp file after adding some Cl- ions using genion. It goes like this: This is unnecessary. Just #include ions.itp and the parameters for Cl- for whatever force field you're using are included. Thanks for the reply. I will try to follow your suggestion, but just for clarification, setting nrexcl=0 will allow nb interaction between all the atoms in a molecule? [ moleculetype ] ; Namenrexcl Cl_ion 0 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1CL- 1Cl- Cl 1 -1 35.453 ; qtot -1 2CL- 2Cl- Cl 2 -1 35.453 ; qtot -2 3CL- 3Cl- Cl 3 -1 35.453 ; qtot -3 To allow nb interactions between all the atoms in the molecule Cl_ion, is setting nrexcl = 0 okay? 2) In spce.itp provided with GROMACS, [ moleculetype ] ; molname nrexcl SOL 2 while in the manual, on pg. 100 (Chapter-5 Topologies) [ moleculetype ] ; molname nrexcl SOL 1 why is the inconsistency? Probably just a typo. So the correct version will be nrexcl=2, which means atoms no more than 2 bonds away will be excluded from nb interactions. Is my undestanding correct? 3) I am using SPC/E water model with GROMOS96 43a1 ff, (SPC is recommended). Since SPC/E is one of the most used model, should I consider using OPLS rather than GROMOS96, otherwise how significant will be the errors? An excellent comparison of different force fields and different water models can be found in: Hess and van der Vegt (2006) J. Phys. Chem. B 110: 17616-17626. 4) I am using GROMOS96 43a1, so am I allowed to change combination rule to '2' ( '1' is the default). How significantly will it affect the simulations? I would say it invalidates everything. The defaults for combination rules, bonded parameters, etc. are as much a part of each force field as the atom types and charges. -Justin Any relevant idea/suggestion/reference is appreciated. Thanks, Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Some questions regarding generating topologies
Manik Mayur wrote: Hi, Even though after going through the manual, I still have some basic confusions regarding generating topologies. 1) I have generated an itp file after adding some Cl- ions using genion. It goes like this: This is unnecessary. Just #include ions.itp and the parameters for Cl- for whatever force field you're using are included. [ moleculetype ] ; Namenrexcl Cl_ion 0 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1CL- 1Cl- Cl 1 -1 35.453 ; qtot -1 2CL- 2Cl- Cl 2 -1 35.453 ; qtot -2 3CL- 3Cl- Cl 3 -1 35.453 ; qtot -3 To allow nb interactions between all the atoms in the molecule Cl_ion, is setting nrexcl = 0 okay? 2) In spce.itp provided with GROMACS, [ moleculetype ] ; molname nrexcl SOL 2 while in the manual, on pg. 100 (Chapter-5 Topologies) [ moleculetype ] ; molname nrexcl SOL 1 why is the inconsistency? Probably just a typo. 3) I am using SPC/E water model with GROMOS96 43a1 ff, (SPC is recommended). Since SPC/E is one of the most used model, should I consider using OPLS rather than GROMOS96, otherwise how significant will be the errors? An excellent comparison of different force fields and different water models can be found in: Hess and van der Vegt (2006) J. Phys. Chem. B 110: 17616-17626. 4) I am using GROMOS96 43a1, so am I allowed to change combination rule to '2' ( '1' is the default). How significantly will it affect the simulations? I would say it invalidates everything. The defaults for combination rules, bonded parameters, etc. are as much a part of each force field as the atom types and charges. -Justin Any relevant idea/suggestion/reference is appreciated. Thanks, Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Some questions regarding generating topologies
Manik Mayur wrote: On Wed, Jun 3, 2009 at 9:04 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Manik Mayur wrote: Hi, Even though after going through the manual, I still have some basic confusions regarding generating topologies. 1) I have generated an itp file after adding some Cl- ions using genion. It goes like this: This is unnecessary. Just #include ions.itp and the parameters for Cl- for whatever force field you're using are included. Thanks for the reply. I will try to follow your suggestion, but just for clarification, setting nrexcl=0 will allow nb interaction between all the atoms in a molecule? Using nrexcl only applies to intramolecular nonbonded interactions. There has to be some reason with nrexcl = 1 is specified for ions in ions.itp, but that may have to do with something in the code. I suppose, in general, nrexcl = 0 would include all interactions, but you probably don't want to do that for most molecules, since, i.e. neighboring (bonded) atoms interact principally through the bonded interaction; nonbonded calculations should not be applied to this atom pair. [ moleculetype ] ; Namenrexcl Cl_ion 0 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1CL- 1Cl- Cl 1 -1 35.453 ; qtot -1 2CL- 2Cl- Cl 2 -1 35.453 ; qtot -2 3CL- 3Cl- Cl 3 -1 35.453 ; qtot -3 To allow nb interactions between all the atoms in the molecule Cl_ion, is setting nrexcl = 0 okay? 2) In spce.itp provided with GROMACS, [ moleculetype ] ; molname nrexcl SOL 2 while in the manual, on pg. 100 (Chapter-5 Topologies) [ moleculetype ] ; molname nrexcl SOL 1 why is the inconsistency? Probably just a typo. So the correct version will be nrexcl=2, which means atoms no more than 2 bonds away will be excluded from nb interactions. Is my undestanding correct? Should be. -Justin 3) I am using SPC/E water model with GROMOS96 43a1 ff, (SPC is recommended). Since SPC/E is one of the most used model, should I consider using OPLS rather than GROMOS96, otherwise how significant will be the errors? An excellent comparison of different force fields and different water models can be found in: Hess and van der Vegt (2006) J. Phys. Chem. B 110: 17616-17626. 4) I am using GROMOS96 43a1, so am I allowed to change combination rule to '2' ( '1' is the default). How significantly will it affect the simulations? I would say it invalidates everything. The defaults for combination rules, bonded parameters, etc. are as much a part of each force field as the atom types and charges. -Justin Any relevant idea/suggestion/reference is appreciated. Thanks, Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar
Re: [gmx-users] PME on BlueGene
Mark Abraham wrote: Jakob Wohlert wrote: Hi, I'm trying to compile Gromacs 4.0.4 for BlueGene/P, and using the configuration options from the wiki I have succeeded insofar that I have a working program as long as I don't use PME. I have tried many different variants of fftw - 2.1.5, 3.2.1, single precision, double precision, different compiler optimizations and so on, but it all ends the same: mdrun getting stuck somewhere in the initialization process. However, by using the built in fft library FFTPACK instead of FFTW, PME will work, but that is not really an alternative. In at least a few cases I have been able to pinpoint the location where it hangs - it's in pme.c, subroutine pme_dd_sendrecv. The program calls MPI_Sendrecv, but then nothing else happens as far as I can tell. I'm confused and I have sort of ran out of ideas right now. Has anyone else encountered a problem like this, or has anyone any suggestions how to proceed from here? Thanks for your answer! That looks to me like the separate PME nodes are dying through some linking problem and the problem is only manifest on node 0 when its sendrecv doesn't complete. Forcing mdrun -npme 0 may confirm this when all the nodes die at the first point they refer to a symbol in the FFT library. Otherwise, looking at warnings/errors from the linker will be required. Ok, can you be a little more specific? Do you mean when compiling fftw, gromacs or both? I'm not very experienced with these kind of things. Are you compiling an FFT library version for the back end, or the front end? I'm trying to get it to work on the back end, on the front end it works fine! (So, I have fftw libraries for both). /Jakob ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Resizing heterogeneous membrane (POPG/POPE mixture)
Hi Nicolas, I'll try that too since I am somewhat familiar with VMD scripting to I may equilibrate a 2X 2Y 1Z membrane like you specified, and have a script find a timeframe where lipid composition fits what I need. Thanks, -Shay -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Nicolas Sapay Sent: Wednesday, June 03, 2009 15:23 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Resizing heterogeneous membrane (POPG/POPE mixture) Shay Amram a écrit : Dear GROMACS users, I have been trying to expand a membrane by a non-integer multiplier (for example X1.5). This can be done using *genbox -cs Membrane.gro -o Expanded_membrane.gro box 1.5X 1.5Y Z*** This has worked very good with _homogenous_ membranes, and only very short equilibrium times were required to re-equilibrate the membrane (~10-20ns). Now I am trying to deal the same way with _heterogeneous_ membrane (POPG/POPE mixture, Mikko Karttunen et. al). When trying to invoke the above command to the POPG/POPE membrane I get a membrane with different compositions of lipids in the upper and lower leaflets. This happens (so I suspect) because the arrangement of lipids in each leaflet is somewhat different so that the molecules that get' to be multiplied do not conserve the same ratio of different lipids as in the original structure (which has ratio of 1:3 POPG/POPE). Is there a way to multiply the membrane by a _non-integer_ number AND somehow conserve the ratio of different lipid species too? Or at the very least, to have both upper and lower leaflets identical after multiplication? (This, too, would help immensely). This is quite a difficult task unfortunately. Personally, I create a membrane patch larger than the one I want (e.g. 2x 2y 1z), load the gro file into VMD, then cut a patch the size/composition I need. That means doing selections like: set sel [atomselect top same resid as (x... and x... and y... and y...)] Checking the number of lipids in each layer: [atomselect top resname DOPG and name P1 and z... and (same resid as (x... and x... and y... and y...))] num [atomselect top resname DOPG and name P1 and z... and (same resid as (x... and x... and y... and y...))] num Completing the selection by manually adding the residues I need: set sel [atomselect top same resid as (x... and x... and y... and y...) or resid ...] Saving the coordinates: animate write pdb sel $sel This is a tidy task and some equilibration is still required after that. Basic knowledge of TCL/VMD scripting languages may be required to facilitate/automate the work. Nicolas Thanks, -Shay ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Gromacs output analysis
Hello to everybody I need the gromacs analysis document. I mean i want to do analysis (like; RMSD, traj)of my result which I got after simulation of protein molecule. If anybody having any PDF or web link emphasis the analysis part, please forword me... Thank you Rituraj On Wed, Jun 3, 2009 at 9:05 PM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. protein running out of box (sheerychen) 2. Re: protein running out of box (Justin A. Lemkul) 3. Re: protein running out of box (ravi sharma) 4. spc.itp for the amber force field (Rebeca Garc?a Fandi?o) 5. Some questions regarding generating topologies (Manik Mayur) 6. Re: Some questions regarding generating topologies (Justin A. Lemkul) -- Message: 1 Date: Wed, 3 Jun 2009 15:37:57 +0200 From: sheerychen sheeryc...@gmail.com Subject: [gmx-users] protein running out of box To: gmx-users@gromacs.org Message-ID: e1b92dfb0906030637y6cc57951oaf959aafd2b46...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hello, every body. I have running a MD for 10ns. However, after 5ns part of protein will running out of the box and be located at other part of the water box. And the whole structure seems ver strange. It seems that it was caused by the mass translation but I have used the comm_mode=Linear. Any suggestions? -- Zhen Chen, Department of Bioprocess and Biosystem Engineering, Hamburg University of Technology, Denickestr. 15, D-21071, Hamburg,Germany Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: zhen.c...@tuhh.de -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090603/20c8cd2e/attachment-0001.html -- Message: 2 Date: Wed, 03 Jun 2009 09:46:08 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] protein running out of box To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a267ea0.8090...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed sheerychen wrote: Hello, every body. I have running a MD for 10ns. However, after 5ns part of protein will running out of the box and be located at other part of the water box. And the whole structure seems ver strange. It seems that it was caused by the mass translation but I have used the comm_mode=Linear. Any suggestions? What you are seeing is a normal consequence of periodicity. There is no side in an infinite system: http://oldwiki.gromacs.org/index.php/Periodic_Boundary_Conditions -Justin -- Zhen Chen, Department of Bioprocess and Biosystem Engineering, Hamburg University of Technology, Denickestr. 15, D-21071, Hamburg,Germany Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: zhen.c...@tuhh.de mailto:zhen.c...@tuhh.de ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Message: 3 Date: Wed, 3 Jun 2009 07:07:57 -0700 (PDT) From: ravi sharma rdsharma...@yahoo.com Subject: Re: [gmx-users] protein running out of box To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 147031.55861...@web54606.mail.re2.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Dear Zhen Chen Protein is located stranger(sometime at the one side of the protein,in other frame other side). Its not a problem. Your simulation is fine. it is due to you had given PBC. thats why. You can reset your trejectory using trjconv. regards Ravi Datta Sharma Lecturer, Bioinformatics, Department of Microbiology, CCS Unversity, Meerut --- On Wed, 3/6/09, sheerychen sheeryc...@gmail.com wrote: From
Re: [gmx-users] Gromacs output analysis
You should have a look at the manual/wiki/online documentation. You'll find everything you need. On Jun 3, 2009, at 8:28 PM, rituraj purohit wrote: Hello to everybody I need the gromacs analysis document. I mean i want to do analysis (like; RMSD, traj)of my result which I got after simulation of protein molecule. If anybody having any PDF or web link emphasis the analysis part, please forword me... Thank you Rituraj On Wed, Jun 3, 2009 at 9:05 PM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. protein running out of box (sheerychen) 2. Re: protein running out of box (Justin A. Lemkul) 3. Re: protein running out of box (ravi sharma) 4. spc.itp for the amber force field (Rebeca Garc?a Fandi?o) 5. Some questions regarding generating topologies (Manik Mayur) 6. Re: Some questions regarding generating topologies (Justin A. Lemkul) -- Message: 1 Date: Wed, 3 Jun 2009 15:37:57 +0200 From: sheerychen sheeryc...@gmail.com Subject: [gmx-users] protein running out of box To: gmx-users@gromacs.org Message-ID: e1b92dfb0906030637y6cc57951oaf959aafd2b46...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hello, every body. I have running a MD for 10ns. However, after 5ns part of protein will running out of the box and be located at other part of the water box. And the whole structure seems ver strange. It seems that it was caused by the mass translation but I have used the comm_mode=Linear. Any suggestions? -- Zhen Chen, Department of Bioprocess and Biosystem Engineering, Hamburg University of Technology, Denickestr. 15, D-21071, Hamburg,Germany Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: zhen.c...@tuhh.de -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090603/20c8cd2e/attachment-0001.html -- Message: 2 Date: Wed, 03 Jun 2009 09:46:08 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] protein running out of box To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a267ea0.8090...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed sheerychen wrote: Hello, every body. I have running a MD for 10ns. However, after 5ns part of protein will running out of the box and be located at other part of the water box. And the whole structure seems ver strange. It seems that it was caused by the mass translation but I have used the comm_mode=Linear. Any suggestions? What you are seeing is a normal consequence of periodicity. There is no side in an infinite system: http://oldwiki.gromacs.org/index.php/Periodic_Boundary_Conditions -Justin -- Zhen Chen, Department of Bioprocess and Biosystem Engineering, Hamburg University of Technology, Denickestr. 15, D-21071, Hamburg,Germany Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: zhen.c...@tuhh.de mailto:zhen.c...@tuhh.de ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Message: 3 Date: Wed, 3 Jun 2009 07:07:57 -0700 (PDT) From: ravi sharma rdsharma...@yahoo.com Subject: Re: [gmx-users] protein running out of box To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 147031.55861...@web54606.mail.re2.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Dear Zhen Chen Protein is located stranger(sometime at the one side of the protein,in other frame other side). Its not a problem. Your simulation is fine. it is due to you had given PBC. thats why. You can reset your trejectory using trjconv. regards Ravi Datta Sharma Lecturer, Bioinformatics, Department of Microbiology, CCS
Re: [gmx-users] Gromacs output analysis
rituraj purohit wrote: Hello to everybody I need the gromacs analysis document. I mean i want to do analysis (like; RMSD, traj)of my result which I got after simulation of protein molecule. If anybody having any PDF or web link emphasis the analysis part, please forword me... Chapter 8 of the manual contains information on all of the analysis programs. -Justin Thank you Rituraj On Wed, Jun 3, 2009 at 9:05 PM, gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org mailto:gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org mailto:gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. protein running out of box (sheerychen) 2. Re: protein running out of box (Justin A. Lemkul) 3. Re: protein running out of box (ravi sharma) 4. spc.itp for the amber force field (Rebeca Garc?a Fandi?o) 5. Some questions regarding generating topologies (Manik Mayur) 6. Re: Some questions regarding generating topologies (Justin A. Lemkul) -- Message: 1 Date: Wed, 3 Jun 2009 15:37:57 +0200 From: sheerychen sheeryc...@gmail.com mailto:sheeryc...@gmail.com Subject: [gmx-users] protein running out of box To: gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: e1b92dfb0906030637y6cc57951oaf959aafd2b46...@mail.gmail.com mailto:e1b92dfb0906030637y6cc57951oaf959aafd2b46...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hello, every body. I have running a MD for 10ns. However, after 5ns part of protein will running out of the box and be located at other part of the water box. And the whole structure seems ver strange. It seems that it was caused by the mass translation but I have used the comm_mode=Linear. Any suggestions? -- Zhen Chen, Department of Bioprocess and Biosystem Engineering, Hamburg University of Technology, Denickestr. 15, D-21071, Hamburg,Germany Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: zhen.c...@tuhh.de mailto:zhen.c...@tuhh.de -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090603/20c8cd2e/attachment-0001.html -- Message: 2 Date: Wed, 03 Jun 2009 09:46:08 -0400 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] protein running out of box To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4a267ea0.8090...@vt.edu mailto:4a267ea0.8090...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed sheerychen wrote: Hello, every body. I have running a MD for 10ns. However, after 5ns part of protein will running out of the box and be located at other part of the water box. And the whole structure seems ver strange. It seems that it was caused by the mass translation but I have used the comm_mode=Linear. Any suggestions? What you are seeing is a normal consequence of periodicity. There is no side in an infinite system: http://oldwiki.gromacs.org/index.php/Periodic_Boundary_Conditions -Justin -- Zhen Chen, Department of Bioprocess and Biosystem Engineering, Hamburg University of Technology, Denickestr. 15, D-21071, Hamburg,Germany Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: zhen.c...@tuhh.de mailto:zhen.c...@tuhh.de mailto:zhen.c...@tuhh.de mailto:zhen.c...@tuhh.de ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry
Re: [gmx-users] g_dist: extract distances between any two atom pairs
Justin A. Lemkul skrev: Joern Lenz wrote: Dear Gromacs Users, I need to extract all possible distances between any two atom pairs of a small hexa- to dodecamer from a trajectory. The same is necessary for all dihedral angles of this protein. Now I wonder if this is possible without defining all of them manually in the ndx file and call g_dist for each of them ? Is there a short answer on that ? Maybe I missed the answer to that question in the forum ?! Actually, this is one reason why open source is such a fantastic thing! With a little C-skill that functionality ought to be relatively simple to incorporate in some existing analysis tool. Not saying that it takes less time than scripting multiple calls to g_dist, but it can be reused in the future. That level of detail might just require some iterative calls to g_dist and g_angle, unfortunately. Scripts are your friend, here. Also, g_mdmat might be useful, but it plots minimum distances between *residue* pairs, not atom pairs. Much more convenient than repeated calls to g_dist, however :) -Justin greetings, joern ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] ??using pull code when orientation of system changes during MD??
Greetings gromacs users-- I'm using the pull code to calculate the binding affinity of a small drug molecule to DNA, and I have a concern. Does the pull code (see my pull.ppa below) account for the fact that the DNA rotates/translates during MD, and therefore the x- y- and z- directions of pulling are changing with time? verbose = no runtype = afm group_1 = drug reference_group = DNA_site reftype = com afm_k1 = 1000 Have a great day, Dayle Smith Department of Physics Whitman College Walla Walla, WA, USA ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] spc.itp for the amber force field
Rebeca García Fandiño wrote: Hi, I am trying to simulate a system using the parameters for ions developed by Joung et al. and implemented in Amber (frcmod.ionsjc_spce). I have the topology and the crd file. Now, I want to obtain the topology for Gromacs using amb2gmx.pl, so I must change the default parameters (for tip3p) included in amb2gmx.pl. I have seen that in the .tar file ffamber_v4.0 there is no a corresponding itp file for spc model of water in amber, so what parameters should I include for the section of bondtypes, angletypes, atoms, bonds, angles, settles,...? Those corresponding to the SCP in Gromacs directly? Maybe. The required form for the nonbonded parameters depends on combination rules in force. First you should find out if SPC should work with AMBER, because literature that says that will probably also specify the parameters. Perhaps simpler is use amb2gmx.pl to convert the non-solvent part, and then solvate with genbox and add ions with genion later. You'd still need SPC parameters for AMBER however. Mark Thank you very much for your help. Best wishes, Rebeca Garcia Academic Visitor Oxford University Charlas más divertidas con el nuevo Windows Live Messenger http://download.live.com ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] PME on BlueGene
Jakob Wohlert wrote: Mark Abraham wrote: Jakob Wohlert wrote: Hi, I'm trying to compile Gromacs 4.0.4 for BlueGene/P, and using the configuration options from the wiki I have succeeded insofar that I have a working program as long as I don't use PME. I have tried many different variants of fftw - 2.1.5, 3.2.1, single precision, double precision, different compiler optimizations and so on, but it all ends the same: mdrun getting stuck somewhere in the initialization process. However, by using the built in fft library FFTPACK instead of FFTW, PME will work, but that is not really an alternative. In at least a few cases I have been able to pinpoint the location where it hangs - it's in pme.c, subroutine pme_dd_sendrecv. The program calls MPI_Sendrecv, but then nothing else happens as far as I can tell. I'm confused and I have sort of ran out of ideas right now. Has anyone else encountered a problem like this, or has anyone any suggestions how to proceed from here? Thanks for your answer! That looks to me like the separate PME nodes are dying through some linking problem and the problem is only manifest on node 0 when its sendrecv doesn't complete. Forcing mdrun -npme 0 may confirm this when all the nodes die at the first point they refer to a symbol in the FFT library. Otherwise, looking at warnings/errors from the linker will be required. Ok, can you be a little more specific? Do you mean when compiling fftw, gromacs or both? I'm not very experienced with these kind of things. GROMACS links with the FFTW library, so there ought to be warnings of potential problems at link time, i.e. the final stage of a GROMACS make mdrun (having started with a clean configuration, either freshly unpacked or after make clean). The last 100 or so lines of the output of make mdrun should have any relevant data. Are you compiling an FFT library version for the back end, or the front end? I'm trying to get it to work on the back end, on the front end it works fine! (So, I have fftw libraries for both). My BG/L FFTW-3.2 configure line is ../configure --prefix /hpc/home/mja163/progs CC=blrts_xlc --host=powerpc --build=ppc64 CFLAGS=-qbgl -qarch=440d -qtune=440 -qnoautoconfig -O5 --disable-fortran --enable-float but you may need to tweak that for BG/P for all I know. Let me know when/if something works and I'll update the wiki. Mark ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] about PMF calculation
Dear All: I want to do some PMF (Potenial of Mean Force) calculation by AFM pulling method using the pull code to study the unbinding of a protein and a ligand. I want pull the ligand from its binding site and calculate the PMF of the procedure, does it possible? I have read the user manual about PMF calculation carefully, but still not clear how to do . Does anyone have any tutorial about how to do this kind of calculation or any published papers doing this things? anyhelp is greatly appreciate! Best Wishes R-X Gu ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
