[gmx-users] gmx traj ekrot : too many iterations in routine JACOBI

ekr; ekt only works fine. The rotational kinetic energy calculation seems to be the problem. I couldn't find a similar problem in the mailing list. Thanks for your answers. Best, Marlon Sidore 06.69.24.81.94 PhD - Post-doctoral fellow Institut d’Électronique et des Systèmes (UMR 5214) 860

Re: [gmx-users] Normal mode segmentation fault - memory problem ?

Hopefully I'm answering the right way. It also didn't work when using "-last 82737" and the segfault happened right after "will try to allocate memory and convert to full matrix representation". I don't get what I'm doing wrong here. Best, Marlon Sid

[gmx-users] Normal mode segmentation fault - memory problem ?

trict the analysis on the backbone (somehow) if it's a memory problem ? I'm still allocacating 100G to this analysis, I naively thought it was enough. Best, Marlon Sidore PhD - Post-doctoral fellow Institut d’Électronique et des Systèmes -- Gromacs Users mailing list * Please search

[gmx-users] Box shape changing from rectangle to parallelogram at NVT

since eduroam won't let me use another image hosting site: https://drive.google.com/open?id=1PKtivk4lSygMgWey-N5PGhwGZ3JQJJw_ Best regards, Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR7255 31, Chemin Joseph Aiguier 13402 cedex 20 Ma

Re: [gmx-users] em and nvt problem

You can try to reduce emtol in your minimization parameters or start your nvt at a different, lower, temperature. Best, Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR7255 31, Chemin Joseph Aiguier 13402 cedex 20 Marseille France 2017-

Re: [gmx-users] Problem with MD simulation

Hi, you forgot about periodic boundary conditions - you need to put your trajectory through trjconv -pbc mol to make your protein whole again. On Apr 19, 2017 12:45 PM, "Mariusz Wierzbowski" wrote: > Hi, I am not sure if this is a problem. I performed md run for a > protein(pdb code 1rep) and I

Re: [gmx-users] Regarding trajectories

Hello, You want to use trjcat to concatenate all your trajectories. http://manual.gromacs.org/programs/gmx-trjcat.html Regards, Marlon Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR7255 31, Chemin Joseph Aiguier 13402 cedex 20 Mars

Re: [gmx-users] usage trjconv in membrane simulation

Hello, I had success with membrane simulations with: 1) -pbc nojump 2) -center 3) -pbc mol 4) -fit rot+trans This usually works to have the protein fitted and centered. Best regards, Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR72

Re: [gmx-users] Gromacs Learning

You will probably use the martini force field. Once you get used to Gromacs with the tutorials, head to this site and be familiar with the insane.py script. You'll probably make all your CG systems with this (and maybe with daft if you need to put multiple proteins). http://md.chem.rug.nl/ M

Re: [gmx-users] The Berendsen thermostat does not generate the correct kinetic energy distribution.

ly already use v-rescale for the production run). Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR7255 31, Chemin Joseph Aiguier 13402 cedex 20 Marseille France 2016-11-28 11:17 GMT+01:00 Diogo Vila Viçosa : > I guess the best way to u

Re: [gmx-users] output file format under pbc

Hello, If you want your molecule whole, the -pbc mol option of trjconv is probably what you're searching for. Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR7255 31, Chemin Joseph Aiguier 13402 cedex 20 Marseille France 2016-08-26

Re: [gmx-users] Remove PDB and center the protein.

and what you want to analyze), but yeah if the visualization of your trajectory is fine it should be fine. I know I had problems centering on an oligomeric protein in the past, and I had to use -pbc nojump before centering, and then putting everything back in the box with -pbc mol (in 3 rounds of trjc

Re: [gmx-users] Remove PDB and center the protein.

ystem, put everything back in the box: gmx trjconv -s inp.tpr -f nopbc_center.xtc -o center.xtc -pbc mol If you also later want to fit the rotations of your centered thing, you'll want to do it after this too. Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromo

Re: [gmx-users] Creating topology for Cu-containing enzyme, GROMOS96 force field.

ple. Hope that helps. Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR7255 31, Chemin Joseph Aiguier 13402 cedex 20 Marseille France 2016-08-10 21:26 GMT+02:00 Francesca Lønstad Bleken < francescal.ble...@sintef.no>: > I am inter

Re: [gmx-users] protein and ligand is not forming complex after completing simulation

system for all outputs for centering (the first of the second command) you should probably select protein Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR7255 31, Chemin Joseph Aiguier 13402 cedex 20 Marseille France 2016-07-27 17:25 G

Re: [gmx-users] protein and ligand is not forming complex after completing simulation

pbc nojump trjconv_d -s md_0_1.tpr -f trj0.xtc -n index.ndx -o trj1.xtc -center [[Here center on your protein for example]] trjconv_d -s md_0_1.tpr -f trj1.xtc -n index.ndx -o trj2.xtc -pbc mol Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR

Re: [gmx-users] protein and ligand is not forming complex after completing simulation

fails when trying to use trjconv only once, instead of 3 times like this. Hope this helps Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR7255 31, Chemin Joseph Aiguier 13402 cedex 20 Marseille France 2016-07-27 14:26 GMT+02:00 Swagata

Re: [gmx-users] Masses and atomic radii for SASA

Hello, You need to add the radii of your unique atoms in the vdwradii.dat file, which gmx sasa reads. Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR7255 31, Chemin Joseph Aiguier 13402 cedex 20 Marseille France 2016-07-25 8:05 GMT+

Re: [gmx-users] Conversion between nonbonded charmm NBFIX and gromacs cross terms

ually doesn't seem to crash at all on gromacs. Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR7255 31, Chemin Joseph Aiguier 13402 cedex 20 Marseille France 2016-07-22 16:27 GMT+02:00 Kroon, P.C. : > As an aside: Martini forcefi

Re: [gmx-users] Conversion between nonbonded charmm NBFIX and gromacs cross terms

Thanks for your answer, that solved everything. Marlon Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR7255 31, Chemin Joseph Aiguier 13402 cedex 20 Marseille France 2016-07-21 14:01 GMT+02:00 Justin Lemkul : > > > On 7/21/16 5

[gmx-users] Conversion between nonbonded charmm NBFIX and gromacs cross terms

. But I'm currently stuck at how to translate the former into the latter, as it doesn't seem like a simple scaling - since in this example 2 numbers from CHARMM are the same while none are the same in GROMACS. Thanks for your help Marlon Sidore PhD Student Laboratoire d'Ingéni

Re: [gmx-users] charge of aminoacids in an special pH

You can change the protonation state of amino acids with pdb2gmx -inter option. It will ask you the protonation state of every AA. You could also start with a tool like propka in order to know which ones are protonated. Best regards, Marlon Sidore PhD Student Laboratoire d'Ingénieri

Re: [gmx-users] (no subject)

Hello, You can give gmx rms an index file with -n Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR7255 31, Chemin Joseph Aiguier 13402 cedex 20 Marseille France 2016-06-21 10:44 GMT+02:00 Sepideh Momeninezhad < sepideh.momeninez...@g

Re: [gmx-users] converting the frcmod file and off file to gromacs

example from the amber forcefield in amber format and its equivalent in gromacs format, before applying that conversion on your new parameters. Hope that helps. Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR7255 31, Chemin Joseph Aiguier

Re: [gmx-users] grompp not enough parameters

Thanks a lot ... I feel really dumb here ~~ Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR7255 31, Chemin Joseph Aiguier 13402 cedex 20 Marseille France 2016-06-15 17:26 GMT+02:00 Justin Lemkul : > > > On 6/15/16 11:07 AM,

[gmx-users] grompp not enough parameters

quot; I don't understand where there are missing parameters. Indeed, a classical line from the dihedrals of ffbonded.itp has the same number of parameters, for example: " C N CT C 9 180.0 1.44390 2 ; Amber03" Did any of you run into this before ? Best regards,

Re: [gmx-users] Non-neutral system with iron-sulfur clusters

o the previous S in CYS. Simply adding them and the other atoms from CYS (4x in case of the CYS atoms) doesn't yield an integer. I didn't count S and CB twice either. The resulting charge from the whole 4CYS-4Fe-4S is -1.233684. Marlon Sidore PhD Student Laboratoire d'Ing

[gmx-users] Non-neutral system with iron-sulfur clusters

uld I worry ? 1. Smith, D. M. A., Xiong, Y., Straatsma, T. P., Rosso, K. M. & Squier, T. C. Force-Field Development and Molecular Dynamics of [NiFe] Hydrogenase. J. Chem. Theory Comput. 8, 2103–2114 (2012). Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculai

Re: [gmx-users] trjconv -dump buffer overflow

It happens even with the first frame of the .xtc Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR7255 31, Chemin Joseph Aiguier 13402 cedex 20 Marseille France 2016-05-31 19:35 GMT+02:00 Mark Abraham : > Hi, > > It's h

[gmx-users] trjconv -dump buffer overflow

lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f70e1f00ccc] ... """ Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR7255 31, Chemin Joseph Aiguier 13402 cedex 20 Marseille France -- Gromacs Users mailing list * Please s

Re: [gmx-users] Simulation of the membrane protein using Martini. MDP options

Hi, If you're using Gromacs 5.x, I suggest using the mdp options from these files: http://md.chem.rug.nl/index.php/mdp5 The paper associated with these is here: http://www.sciencedirect.com/science/article/pii/S0010465515003628 Best regards Marlon Sidore PhD Student Laboratoire d'

Re: [gmx-users] System blowing up at restart

It actually went on a few steps before blowing up, it didn't blow up directly at restart. Does that mean it simply blew up because of the system ? It always blows up a little time after restarting though, and that's strange given the time it ran the first time. gmx dump doesn't say anything specia