[gmx-users] how to include Fe-S topology in .rtp file

hi all...   I am simulating a protein with Fe-S cluster. What is the protocol for generating a .rtp file with Fe-S topology...As i am using ffG43a1 forcefield.. i searched FFG43a1bon.itp file for Fe-S bond, angle and dihedral type... but it is not there..what i should do?..   If anyone have the

Re: [gmx-users] Nonrepeatable results for gromacs 4.0.5

Hi, For the record there is also the -reprod (reproducibility) that also turns off the dynamic FFTW plan optimization. With these options enabled you will lose a bit of performance, but should get binary identical runs even in parallel (as long as you use the same number of CPUs).

[gmx-users] problem in running grompp

hi i am simulating a membrane protein in POPC bilayer and for that i am following justin's tutorial.it's a nice tutorial and is really helpful. but i'm facing some problems in running the grompp command. after the solvation when i am going to run grompp, it is generting an error as follows

Re: [gmx-users] PME nodes

On Jun 6, 2009, at 1:20 PM, XAvier Periole wrote: On Jun 6, 2009, at 1:08 PM, Justin A. Lemkul wrote: XAvier Periole wrote: Dears, I am having troubles finding the better balance between the PME CPUs and the rest. I played with the rdd, rcon and -npme options but nothing really

[gmx-users] PME nodes

Hello, How can I compile the g_tune_pme program available at: http://www.mpibpc.mpg.de/home/grubmueller/projects/MethodAdvancements/Gromacs/ Many thanks, Andrei ___ gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] problem in running grompp

Samik Bhattacharya wrote: hi i am simulating a membrane protein in POPC bilayer and for that i am following justin's tutorial.it's a nice tutorial and is really helpful. but i'm facing some problems in running the grompp command. after the solvation when i am going to run grompp, it is

Re: [gmx-users] how to include Fe-S topology in .rtp file

amri ta wrote: hi all... I am simulating a protein with Fe-S cluster. What is the protocol for generating a .rtp file with Fe-S topology...As i am using ffG43a1 forcefield.. i searched FFG43a1bon.itp file for Fe-S bond, angle and dihedral type... but it is not there..what i should do?..

Re: [gmx-users] PME nodes

Hi, it's written at the begin of the .c file: * You can compile this tool using the Gromacs Makefile from the * share/gromacs/template directory, just replace 'template' by 'g_tune_pme' * where needed. To enable shell completions for g_tune_pme, just * copy the provided completion.*

RE: [gmx-users] Nonrepeatable results for gromacs 4.0.5

If you turn off dlb this should not happen. Please try it and report if you see the same effect without. No, I do not see the same effect if I turn off dlb. However, I am concerned that the magnitude of the differences between runs exceeds the expected, normal variability (as defined by the

Re: [gmx-users] Nonrepeatable results for gromacs 4.0.5

jimkress_58 skrev: If you turn off dlb this should not happen. Please try it and report if you see the same effect without. No, I do not see the same effect if I turn off dlb. However, I am concerned that the magnitude of the differences between runs exceeds the expected, normal

Re: [gmx-users] about epsion_surface

lammps lammps wrote: Dear, I do not know where should I have to use the epsion_surface? The system include a CG membrane, a charged macromolecule above the membrane and some counterions ? It is suitable to using this parameter epsilon_surface = 1? It is appricated if some one tell me

[gmx-users] gromacs on glacier

Hi, I had the chance to run the GROMACS 4.0.4 on another cluster. Same problem still persists. But what I found is that it can be run on a node with 2 CPUs, but as soon as the number of nodes are increased to 2, 3, . it will crash. Following are the last lines reported in different files: In the

[gmx-users] Energies in simulation

Hi, I am using my own water model which I developed its .itp file. When simulation is done after 1ns and energy is kinetic and potential energies are analyzed, the kinetic value is almost OK, but the potential energy is almost half of the value reported in literature and another MD code that I am

Re: [gmx-users] Energies in simulation

Payman Pirzadeh wrote: Hi, I am using my own water model which I developed its .itp file. When simulation is done after 1ns and energy is kinetic and potential energies are analyzed, the kinetic value is almost OK, but the potential energy is almost half of the value reported in literature

RE: [gmx-users] Energies in simulation

To the best of my knowledge no, but how can I check that? -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: June 8, 2009 11:06 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energies in

Re: [gmx-users] Energies in simulation

Payman Pirzadeh wrote: To the best of my knowledge no, but how can I check that? A. read the original paper: is your topology correct? Are the simulation parameters the same? B. post the itp file here and mdp file and specify energy and expected energy. How about energy units?

Re: [gmx-users] gromacs on glacier

Payman Pirzadeh wrote: Hi, I had the chance to run the GROMACS 4.0.4 on another cluster. Same problem still persists. But what I found is that it can be run on a node with 2 CPUs, but as soon as the number of nodes are increased to 2, 3, … it will crash. Following are the last lines

RE: [gmx-users] Energies in simulation

Here is the content of .itp file which I developed: ; This is an itp file to describe water's six-site model by H. Nada and J.P. J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413 (2003) ; This model is a combination of TIP4P and TIP5P. It has three LJ sites and 3 Coulomb sites ;

Re: [gmx-users] Energies in simulation

Payman Pirzadeh wrote: Here is the content of .itp file which I developed: ; This is an itp file to describe water's six-site model by H. Nada and J.P. J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413 (2003) ; This model is a combination of TIP4P and TIP5P. It has three LJ sites

RE: [gmx-users] gromacs on glacier

Hi Justin, Since the manual itself was not sufficient, I asked some other people who are running GROMACS in our group (but they run only on 2 CPUs). Here are the steps I took to compile the parallel version (I have included my notes that they told me as well): Installation 1. ./configure

RE: [gmx-users] Energies in simulation

Well, when I set the box, I used 'editconf' command to rescale the box to have the right density which was ~997. After simulation, I got the following: Energy Average RMSD Fluct. Drift Tot-Drift

Re: [gmx-users] gromacs on glacier

Payman Pirzadeh wrote: Hi Justin, Since the manual itself was not sufficient, I asked some other people who are running GROMACS in our group (but they run only on 2 CPUs). Here are the steps I took to compile the parallel version (I have included my notes that they told me as well):

Re: [gmx-users] Energies in simulation

Payman Pirzadeh wrote: Well, when I set the box, I used 'editconf' command to rescale the box to have the right density which was ~997. After simulation, I got the following: Energy Average RMSD Fluct. Drift Tot-Drift

RE: [gmx-users] gromacs on glacier

Dear Justin, Here is the mpich version: MPICH Version: 1.2.7p1 MPICH Release date: $Date: 2005/11/04 11:54:51$ MPICH Patches applied: none MPICH configure:-prefix=/share/apps/intel/mpich/ MPICH Device: ch_p4 Also the gcc compiler: gcc (GCC) 3.4.6 20060404 (Red Hat

RE: [gmx-users] Energies in simulation

Well, I tried to equilibrate the system, and I think the program has included all the distortion that the system had been through. When I checked the trajectory, the box was highly distorted as the simulation started, then returned to its cubic shape. Also, I am a bit confused by the word strange.

Re: [gmx-users] gromacs on glacier

Payman Pirzadeh wrote: Dear Justin, Here is the mpich version: MPICH Version: 1.2.7p1 MPICH Release date: $Date: 2005/11/04 11:54:51$ MPICH Patches applied: none MPICH configure:-prefix=/share/apps/intel/mpich/ MPICH Device: ch_p4 Well, I think that MPICH is

[gmx-users] best way to generate .pdb files?

I am currently using chembiodraw to draw my molecular structure but it does not generate an adequate pdb file. what is the best way to make them? i feel like my only hold back right now is the pdb file. thank you for your help :)

Re: [gmx-users] best way to generate .pdb files?

Joseph Johnson wrote: I am currently using chembiodraw to draw my molecular structure but it does not generate an adequate pdb file. what is the best way to make them? i feel like my only hold back right now is the pdb file. Search the PDB for available ligands, or use the JME editor

[gmx-users] Suggestion for g_tune_pme

A small suggested change to g_tune_pme. Allowing the specification of the executable on all the nodes would be appreciated since I (at least) follow the suggestion in the installation directions and suffix my parallel version of mdrun with _mpi, so the executable is mdrun_mpi, not mdrun. You

RE: [gmx-users] Suggestion for g_tune_pme

Actually, I was incorrect about the use of MPI commands. As a matter of fact, if you don't have your default hostfile set up properly, you will get incorrect results since g_tune_pme will only look at the one node on which you started it. Jim -Original Message- From:

[gmx-users] zero surface tension

Hello everyone, In the literature, Many reports use the lateral and normal pressures independently coupled to a pressure of 1 bar for bio-membrane simulations. I want to know whether it can guarantee the zero surface tension of the membrane. If not, which situation it can not guarantee. Any

[gmx-users] problem with trjconv

Dear all I am on the final step of MD simulation of membrane protein . the final mdrun has successfully completed after that I have filtered the water from the system .next step is to convert it in final pdb to view it in pymol for this I am using trjconv in this step I

Re: [gmx-users] problem with trjconv

nitu sharma wrote: Dear all I am on the final step of MD simulation of membrane protein . the final mdrun has successfully completed after that I have filtered the water from the system .next step is to convert it in final pdb to view it in pymol for this I am using