Re: [gmx-users] Re:6. QMMM, Segmentation fault (Olga Ivchenko)

Actually I am not sure that I can understand what is thread. But I can paste QMMM file here: title= my_mdp_file cpp = /usr/bin/cpp -traditional include = define = integrator = md tinit=

[gmx-users] group temperatures and kinetic energies

Dear gmx'ers, I am somewhat confused relating temperatures and kinetic energies in gromacs output. I simulate NVE system of N0 rigid molecules in vacuo, 'comm_mode' is set to 'None'. When I check the output 'Kinetic En.' and 'Temperature', the relation between them (see Eq. (3.13) of Manual)

Re: [gmx-users] group temperatures and kinetic energies

I'm awfully sorry for groundless troubling! The sum of group kinetic energies IS STRONGLY EQUAL to the total one. Really I did compared the outputs of DIFFERENT simulations... Dear gmx'ers, I am somewhat confused relating temperatures and kinetic energies in gromacs output. I simulate NVE

[gmx-users] trouble parallelizing a simulation over a cluster

Thanks a lot Justin for the very helpful answers concerning the pressure equilibration. Using Berendsen Barostat over 200 ps has lead to the correct average pressure... I have another issue to discuss with you and with the Gromacs mailing list members; I have been trying to run a simulation

[gmx-users] Re: trouble parallelizing a simulation over a cluster

On Dec 8, 2010, at 1:03 PM, Hassan Shallal wrote: Thanks a lot Justin for the very helpful answers concerning the pressure equilibration. Using Berendsen Barostat over 200 ps has lead to the correct average pressure... I have another issue to discuss with you and with the Gromacs mailing

[gmx-users] -symm option

Dear all does somebody knows how -symm option from g_density command do the calculations? Or in other word what is the basic of -symm option? Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] Hard Spheres

Hi all! I am trying to add some hard spheres to my simulation. As far as i can tell from the manual Gromacs supports only LJ or Buckingham for non-bonded interaction. Is there a way to add hard spheres to lets say a simulation of Water molecules without interfering into the regular water-water

Re: [gmx-users] How to construct user specified bond potential

Jia Haitao wrote: Manual section 4.2.13 maybe not enough. My potential functional shape is much more complex. I need at least two different force constants as C6 and C12 in LJ potential function in section 6.7.2. I use this for block copolymer system. There is only two types of monomer(e.g.

Re: [gmx-users] How to construct user specified bond potential

I have construct two table files: table_b0.xvg for A-A bond, table_b1.xvg for B-B bond. and generated the bonds part of the topology file like this: [ bonds ] ; aiaj funct table_numberk 1 28 01.000 2 38 0

[gmx-users] g_energy: Energy names magic number mismatch

Dear gromacs users, I am facing the following problem while running gromacs 4.5.1 at BlueGene/P supercomputer. The job is submitted by the following script file: #!/bin/sh # # @ account_no = xxx # @ job_name= NVT1 # @ job_type= bluegene # @ output

Re: [gmx-users] How to construct user specified bond potential

Jia Haitao wrote: I have construct two table files: table_b0.xvg for A-A bond, table_b1.xvg for B-B bond. and generated the bonds part of the topology file like this: [ bonds ] ; aiaj funct table_numberk 1 28 01.000 2 38

RE: [gmx-users] g_energy: Energy names magic number mismatch

Hi, There have been some issues with version 4.5.1 and energy files and continuation. But I don't recall them being this fatal. Anyhow, it would be better to upgrade to version 4.5.3, which contains several bug fixes. Berk From: mstu...@slb.com To: gmx-users@gromacs.org Date: Wed, 8 Dec 2010

Re: [gmx-users] g_energy: Energy names magic number mismatch

Mikhail Stukan wrote: Dear gromacs users, I am facing the following problem while running gromacs 4.5.1 at BlueGene/P supercomputer. The job is submitted by the following script file: #!/bin/sh # # @ account_no = xxx # @ job_name= NVT1 # @ job_type

Re: [gmx-users] Umberella sampling

mohsen ramezanpour wrote: Dear All And Specially Dear Justin I read the toturial of Umbrella Sampling.It was very useful But there are afew question,of course about my work . 1-Is it necessary pulling one molecule along the line connecting their COMs? The pull code is based on COM

[gmx-users] Can't build gromacs-4.5.3 with cmake

Hello gmx-users, I am trying to build gromacs-4.5.3 with GPU support with OpenMM. I have followed the INSTALL-GPU instructions along with the tips given in this post: http://www.mail-archive.com/gmx-users@gromacs.org/msg34139.html However, I am receiving the following error from cmake even

Re: [gmx-users] Can't build gromacs-4.5.3 with cmake

What cmake version are you using? On Wed, Dec 8, 2010 at 9:49 AM, Keith Callenberg kmc...@pitt.edu wrote: Hello gmx-users, I am trying to build gromacs-4.5.3 with GPU support with OpenMM. I have followed the INSTALL-GPU instructions along with the tips given in this post:

[gmx-users] COM

Dear All How can I know what is the vector which connect center of mass of two molecules(having their complex pdb file) ? Can I attain it by Gromacs or by Pymol? thanks in advance mohsen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] COM

mohsen ramezanpour wrote: Dear All How can I know what is the vector which connect center of mass of two molecules(having their complex pdb file) ? Can I attain it by Gromacs or by Pymol? Use g_dist. -Justin thanks in advance mohsen --

[gmx-users] g_principal

Hi everyone, I'm trying to use g_principal for the first time. It gives 4 output files: axis1, axis2, axis3 moi.dat My question is: how can I know which axis correponds to the lowest eigenvalue? Nothing is mentioned in the manual. Thank you. Carla -- gmx-users mailing list

[gmx-users] Can't build gromacs-4.5.3 with cmake

I am running cmake version 2.8.0 on Ubuntu 10.04 64-bit with gcc 4.4.3. ~/apps/gromacs-4.5.3$ cmake -version cmake version 2.8.0 Thanks, Keith What cmake version are you using? On Wed, Dec 8, 2010 at 9:49 AM, Keith Callenberg kmc112 at pitt.edu wrote: Hello gmx-users, I am trying to build

Re: [gmx-users] Can't build gromacs-4.5.3 with cmake

Keith Callenberg wrote: I am running cmake version 2.8.0 on Ubuntu 10.04 64-bit with gcc 4.4.3. ~/apps/gromacs-4.5.3$ cmake -version cmake version 2.8.0 Does it make a difference if you build outside the source tree (as is recommended)?

Re: [gmx-users] Can't build gromacs-4.5.3 with cmake

Ah! Outside the source tree to me meant, outside src/. I see now that it means outside gromacs-4.5.3. It does indeed make a difference, now I can build. When I tried to compile with OpenMM I ran into an error that I was missing libxml-2.0. I had libxml2 installed, but I needed to install the

Re: [gmx-users] Replacing charges of a residue, pdb2gmx -rtpo alternative?

On Tue, Dec 7, 2010 at 3:17 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 8/12/2010 4:07 AM, J. Nathan Scott wrote: Hello all! I spent some time searching the archive and can't find an answer to this question. Is there a replacement for the -rtpo option for pdb2gmx? This option is

[gmx-users] Re: correlation function

On 2010-12-08 20.51, samue...@ifi.unicamp.br wrote: Hello Dr. David gromacs calculate correlation function per atom with as velocity autocorrelation function and self - van hove correlation function in long time ( 0.1 microsenconds ) beacuse a work with supercooled liquids, of method

[gmx-users] Regarding parameters of octane box in ffamber99sb - ildn

Hello all I have to create an octane box for studying effect of solvent hydrophobicity on enzyme activation. Anyone using octane parameterized file in amber? Please suggest me how to parameterize it or is there any tutorial for it. As i am a beginner, so plz explain in steps. Thanks a lot.

Re: [gmx-users] Regarding parameters of octane box in ffamber99sb - ildn

YUVRAJ UBOVEJA wrote: Hello all I have to create an octane box for studying effect of solvent hydrophobicity on enzyme activation. Anyone using octane parameterized file in amber? Please suggest me how to parameterize it or is there any tutorial for it. As i am a beginner, so plz explain in

[gmx-users] anaeig

g_anaeig generated numbers of c-alpha or protein structures through -extr extreme.pdb. The bash shell show numbers of eigenvector structures starting from first to last frames are as follows eigenvector Minimum Maximum value time value time

Re: [gmx-users] Hard Spheres

On Wed, Dec 8, 2010 at 4:01 AM, Sascha Hempel sascha.hem...@bci.tu-dortmund.de wrote: Hi all! I am trying to add some hard spheres to my simulation. As far as i can tell from the manual Gromacs supports only LJ or Buckingham for non-bonded interaction. Why cant you use LJ? By setting the

Re: [gmx-users] -symm option

try using to find out, its described on http://manual.gromacs.org/current/online/g_density.html On Wed, Dec 8, 2010 at 4:10 AM, Morteza Khabiri khab...@greentech.czwrote: Dear all does somebody knows how -symm option from g_density command do the calculations? Or in other word what is the

[gmx-users] Re: Re:6. QMMM, Segmentation fault (Olga Ivchenko) (Olga Ivchenko)

Try to run with mdrun -nt 1 1. Re: Re:6. QMMM, Segmentation fault (Olga Ivchenko) (Olga Ivchenko) 2. group temperatures and kinetic energies (Dmitri Dubov) 3. Re: group temperatures and kinetic energies (Dmitri Dubov)

Re: [gmx-users] Hard Spheres

On Wed, Dec 8, 2010 at 4:01 AM, Sascha Hempel sascha.hem...@bci.tu-dortmund.de wrote: Hi all! I am trying to add some hard spheres to my simulation. As far as i can tell from the manual Gromacs supports only LJ or Buckingham for