RE: [gmx-users] Exclusions in topology file seem not working for big systems

Hi, If you really had too many exclusions you would get an error message. So I just tested this. I used the couple_moltype option to couple a 389 atom protein. This generates exclusions between each protein atom and the 388 others. All interactions are excluded correctly (and re-added as

[gmx-users] coarse_grain.tcl script does not show all of the coarse-grained bonds in vmd

Hi all, I was trying to show the bonds between my CG beads in VMD. I have four CG beads per each molecule, and there are 18 separate molecules which contain these four beads, which results in having 72 CG beads in total. Therefore, I expect to see 54 CG bonds in the end. I used the

Re: [gmx-users] coarse_grain.tcl script does not show all of the coarse-grained bonds in vmd

Ozge Engin a écrit : Hi all, I was trying to show the bonds between my CG beads in VMD. I have four CG beads per each molecule, and there are 18 separate molecules which contain these four beads, which results in having 72 CG beads in total. Therefore, I expect to see 54 CG bonds in the

[gmx-users] spatial distribution function (SDF)

Hai all... Did anyone know how to do spatial distribution functions??? I have 125 ion pairs in my system. The problem is, 1)how I can I get the 3-D probability distributions of anion around cation or cation around anion in my system? Could anybody tell me the method? 2)When I read the

[gmx-users] Re: gmx-users Digest, Vol 68, Issue 21

-- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20091203/31581af5/attachment-0001.html -- Message: 3 Date: Thu, 3 Dec 2009 11:23:46 +0200 From: Ozge Engin ozge.en...@gmail.com Subject: [gmx-users] coarse_grain.tcl

[gmx-users] Protonation and solvation software

What is the best software for protonating and for solvating pdb files for doing Molecular Dynamics with GROMACS?. Best regards. Lucio. Lucio Ricardo Montero Valenzuela Instituto de Biotecnologia, UNAM Departamento de Biologia Molecular de Plantas Av. Universidad 2001, Col. Chamilpa

[gmx-users] Re: amber force field in Gromacs

Dear Servaas, Tested again in 'vacuum' and I saw no problems. Here goes what I did: #-- cat EOF | leap.in verbosity 1 source leaprc.ff99SB ad = sequence { DA5 DA DA3 } saveamberparm ad da_amber.top da_amber.crd savepdb ad DA.pdb quit EOF tleap -f leap.in |

[gmx-users] Fatal error: No such moleculetype Na

Hi All, I am trying to run the tutorial http://code.google.com/p/acpypi/wiki/TutorialAcpypi4Gromacs; for using ACPYPI generated topology with GROMACS. I am using amber99sb forcefield for one docked complex. It is running successfully upto genion and giving error while doing grompp for energy

Re: [gmx-users] Fatal error: No such moleculetype Na

vivek sharma wrote: Hi All, I am trying to run the tutorial http://code.google.com/p/acpypi/wiki/TutorialAcpypi4Gromacs; for using ACPYPI generated topology with GROMACS. I am using amber99sb forcefield for one docked complex. It is running successfully upto genion and giving error while

Re: [gmx-users] Re:gmx-users Digest, Vol 67, Issue 150 (memory allocationerror)

hema dhevi wrote: hai justin, ya its robust. and urs is the only tutorial which i found for transmembrane protein MD simulation in GROMACS. Its really useful. thank you. As you said i tried it in other system also there i used gromacs version 3.3.3. i am getting the

Re: [gmx-users] Protonation and solvation software

Lucio Ricardo Montero Valenzuela wrote: What is the best software for protonating and for solvating pdb files for doing Molecular Dynamics with GROMACS?. The Gromacs tools themselves - pdb2gmx allows you to select protonation states and add back any necessary hydrogen atoms when generating

[gmx-users] Reducing Standard Error output

Our first run typically produces this output Getting Loaded... Reading file md.tpr, VERSION 4.0.5 (single precision) Loaded with Money starting mdrun 'Protein in water' 500 steps, 1.0 ps. step 0 step 100, remaining runtime:95 s Fraction complete: 0.2 step 200, remaining

[gmx-users] g_densmap and xpm files

Hi all. I have a question about xpm files produced by g_densmap. I would like, if possible, to extract information in numerical format, such as for example a single txt file with three columns 'x y density' for all the points on the grid chosen. These should be the information which are

[gmx-users] PBC screw

Hello, grompp 4.0.5 gave me the following error message. ERROR: invalid enum 'full' for variable pbc, using 'xyz' Next time use one of: 'xyz' 'no' 'xy' 'screw' Could someone tell me what does the screw option? I cant find it into paper and online manual, as well as at the gmx-list. bests eef

R: [gmx-users] g_densmap and xpm files

In my previous e-mail I was not clear enough... extracting x and y values from xpm is easy and it is also easy to extract the density informations since they are represented by letters and for each of them a corresponding value of the number density is given at the beginning of the file. In my

[gmx-users] spatial distribution function (SDF)

g_spatial -h -or- g_sdf -h -- original message -- ai all... Did anyone know how to do spatial distribution functions??? I have 125 ion pairs in my system. The problem is, 1)how I can I get the 3-D probability distributions of anion around cation or cation around anion in my system?

[gmx-users] Heat of vaporization in gromacs

Hi, Please let me know which of the gromacs utilities is responsible for heat of vaporization calculation. Thanks in advance, Vitaly -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search

Re: [gmx-users] Heat of vaporization in gromacs

Vitaly V. Chaban wrote: Hi, Please let me know which of the gromacs utilities is responsible for heat of vaporization calculation. Thanks in advance, Vitaly g_energy and you. you need liquid and gas phase simulations. -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group,

Re: [gmx-users] Reducing Standard Error output

Thanks, I just figured out removing the -v will reduce output. Interestingly I only have this problem with 64-bit Windows hosts. I have not observed it in any others and I have a fairly diverse environment on this project. For now I can say removing the -v gets the app to finish the run. Jack

[gmx-users] What is the exact difference in the g_energy output between LJ(1-4) LJ(SR) and LJ(LR)?

Hi, As per the title. I need to understand what is the difference to help myself debug my inane efforts at CG parametrization. LJ(1-4) I think is clear (non bonded, non-coulombic interactions between 1-4 pairs described in the topology), but about the rest? thanks! m. -- gmx-users mailing

Re: [gmx-users] Exclusions in topology file seem not working for big systems

Thanks Dr Hess. I didn't get an error message when using grompp, then I think I didn't have too many exclusions. I didn't know about using couple_type in this context before. If I get it correctly, if I want to exclude all non-bonding interactions inside a protein using couple_type, I must

RE: [gmx-users] Exclusions in topology file seem not working for big systems

Hi, I think that for your problem the couple option is not useful. It does exactly the opposite. I removes all interactions of the selected molecule type with the rest of the system and transform all interactions within the molecule by vacuum non-cutoff LJ and Coulomb interactions. (which end

[gmx-users] LIE method

Dear users, I want to estimate the affinity of a protein to two diferent ligands and compare the results. Is the LIE the best method to do that? Does any one have a reference that this kind of analysis is performed or an example of mdp? Best regards, Tatiana -- gmx-users mailing list

Re: [gmx-users] Exclusions in topology file seem not working for big systems

Thank you very much Dr Hess. Then I guess I have to test my rerun workaround that I mentioned for my system. About 1-4 interactions in general, could you a little bit about 1-4 energies while using exclusions please? I hope I am not missing something obvious. The main thing that I am not sure

[gmx-users] topology and rtp file

Hello Gmx Usrs, I am new to Gromacs. I am trying to simulate a protein-membrane complex using  berger-oplsaa combination . I have created a topology file for the protein using pdb2gmx in order to then build up the topology for my system using the include file mechanism. After that I tried to use

Re: [gmx-users] topology and rtp file

irene farabella wrote: Hello Gmx Usrs, I am new to Gromacs. I am trying to simulate a protein-membrane complex using berger-oplsaa combination . I have created a topology Have you properly modified the Berger parameters for use with OPLS-AA? Otherwise, the results you will get will be

[gmx-users] helix tilt

How can I calculate the angle between a helix inserted in a membrane and the axis perpendicular to the surface of the membrane. I have tried using g_helixorient, but the graphs all come as a straight line in zero. Thank you -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] 1-4 interaction energies in g_energy

Hi, Please suggest why is the reason that 1-4 term is not displayed (to be selected for calculation) in the g_energy utility? I have two kinds of objects (with 25 and 5 atoms) in my system - with nexcl equal to 3 and 2. I guess the 1-4 term may not be displayed if there is no 1-4 interactions but

Re: [gmx-users] PBC screw

Hi, please someone correct me if I'm wrong, but the equivalent of Gromacs 3.3.x : pbc = full is pbc = xyz periodic_molecules = yes since Gromacs 4.0. Oliver http://manual.gromacs.org/current/online/mdp_opt.html#nl On Thu, Dec 3, 2009 at 08:22, Eudes Fileti fil...@ufabc.edu.br wrote:

[gmx-users] looking for polar lipid pdb

Grateful for receiving DOPC.pdb file thanks francesco pietra -- gmx-users mailing listgmx-users@gromacs.org http://lists.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

Re: [gmx-users] looking for polar lipid pdb

http://persweb.wabash.edu/facstaff/fellers/ -Justin Francesco Pietra wrote: Grateful for receiving DOPC.pdb file thanks francesco pietra -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry

Re: [gmx-users] Pressure annealing in Gromacs?

Jussi Lehtola wrote: On Thu, 2009-12-03 at 02:30 +1100, Mark Abraham wrote: Jussi Lehtola wrote: I'm experiencing trouble converging the density of some heavy liquid alcohols (after 10 ns of simulation the density is still changing linearly). Is there any way to run pressure annealing in

Re: [gmx-users] helix tilt

Stefan Hoorman wrote: How can I calculate the angle between a helix inserted in a membrane and the axis perpendicular to the surface of the membrane. I have tried using g_helixorient, but the graphs all come as a straight line in zero. See -z in g_sgangle -h Mark -- gmx-users mailing list

Re: [gmx-users] What is the exact difference in the g_energy output between LJ(1-4) LJ(SR) and LJ(LR)?

ms wrote: Hi, As per the title. I need to understand what is the difference to help myself debug my inane efforts at CG parametrization. LJ(1-4) I think is clear (non bonded, non-coulombic interactions between 1-4 pairs described in the topology), but about the rest? See manual 4.6.3 Mark --

Re: [gmx-users] Reducing Standard Error output

Jack Shultz wrote: Thanks, I just figured out removing the -v will reduce output. Interestingly I only have this problem with 64-bit Windows hosts. I have not observed it in any others and I have a fairly diverse environment on this project. For now I can say removing the -v gets the app to

Re: [gmx-users] 1-4 interaction energies in g_energy

Vitaly V. Chaban wrote: Hi, Please suggest why is the reason that 1-4 term is not displayed (to be selected for calculation) in the g_energy utility? I have two kinds of objects (with 25 and 5 atoms) in my system - with nexcl equal to 3 and 2. I guess the 1-4 term may not be displayed if there

RE: [gmx-users] spatial distribution function (SDF)

First three groups are the reference group, from which the SDF is generated, it sets the coordinate system. That means you need to have at least three atoms in the molecule you are generating the SDF from. Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A

Re: [gmx-users] Reducing Standard Error output

yes the environment I was running in was the boinc wrapper and its supposed to somehow return the standard error output. It probably got overloaded. It is curious why I only had the problem on windows 64 but I'm not going to worry about it. On Thu, Dec 3, 2009 at 6:33 PM, Mark Abraham

[gmx-users] Radial distribution specifications

Dear all, I need to plot the radial distribution functions but I am not sure how you specified the different radial pair distribution functions for H2O: gOO, gOH and gHH, in order to have different plots. Please, can you help me out with this? Thank you, Lum -- gmx-users mailing list

Re: [gmx-users] Radial distribution specifications

Lum Nforbi wrote: Dear all, I need to plot the radial distribution functions but I am not sure how you specified the different radial pair distribution functions for H2O: gOO, gOH and gHH, in order to have different plots. Please, can you help me out with this? Use index groups that