Re: [gmx-users] segmentation fault core dumped

On 11/14/19 6:17 AM, Yogesh Sharma wrote: Greetings everyone I was following protein ligand complex tutorial. Given the atom names listed below, you're not doing the tutorial but perhaps are trying to follow its method? There's a big difference. If you're doing something different, you

Re: [gmx-users] defining parameters in a separate itp file

On 11/12/19 6:30 PM, Dave M wrote: Hi Justin, I am having troubles now with domain decompositions when I use openMPI mpirun but it works fine when I run on single mpi. My system is quite large (80x80x80) and I defined additional bonds in top file as: [ intermolecular_interactions ] [

Re: [gmx-users] How to produce "gro" format for calcite {1014} structure.

On 11/14/19 4:03 AM, Najamuddin Memon wrote: Please obtain topology of calcite (1014) from prodrg and you can also see protein-ligand simulation protocol of gromacs exactly follow it. PRODRG produces topologies of very poor quality and does not support calcium. -Justin On Tue, Nov 12,

[gmx-users] Segmentation fault using gmx solvent

Hi all, I've been fighting a particularly painful problem with a system I'm building in Gromacs. gmx mdrun (grompp worked on the system) has been throwing a segmentation fault on my collagen system in a vacuum. Shortly after, I tried gmx solvate but that too was also throwing a segmentation

Re: [gmx-users] slurm, gres:gpu, only 1 GPU out of 4 is detected

Hi, gmx can only detect devices that are visible to it. Your use of slurm is making only one device visible, so gmx can't understand what you mean with -gpu_id 1. But you don't need to manage the same thing twice. If gmx can only see one device and --gres won't allocate a previously allocated

Re: [gmx-users] Question about switching off non-bonded interactions between two molecules for MD simulation

Hi, As far as I understood, you have a protein and ligand (not covalently bonded) and you want to switch off the interaction between one aminoacid and the ligand. Concerning approach 1, If you have a merged topology (only one topology file with one [molecular type] in your case protein and

[gmx-users] helping increasing box

Dear all, I am doing COM-pulling simulations between two lysine chains connected with a surfactant. Basically I want to find the force able to separate the two chains. Increasing the force, at some point gromacs was complaining that the distance between the two pull groups is larger that

Re: [gmx-users] Segmentation fault using gmx solvent

Hi, gmx solvate shouldn't segfault based on a minor change to the input coordinates, so it's probably a bug to look into. Please open an issue at https://redmine.gromacs.org and attach inputs with a failing gmx command, and someone can likely provide some insight! Mark On Thu, 14 Nov 2019 at

Re: [gmx-users] helping increasing box

Hi, What you see, is the effect of boundary condition.To avoid this visualization effect, before increasing the box, you may want to check that your system is whole and better center in the gro file. Best regards Alessandra . On Thu, Nov 14, 2019 at 10:28 PM Giuseppe R Del Sorbo wrote: >

Re: [gmx-users] defining parameters in a separate itp file

Hi Justin, Thanks, I just posted redmine issue #3204. Will try pull code. On Thu, Nov 14, 2019 at 6:02 AM Justin Lemkul wrote: > > > On 11/12/19 6:30 PM, Dave M wrote: > > Hi Justin, > > > > I am having troubles now with domain decompositions when I use openMPI > > mpirun but it works fine

[gmx-users] applied electirc field with use potential

Hi, I have a system with a user-potential. -Can I use an external applied field? -Can I modify my user potential to include the external field? thank you for help, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] How to produce "gro" format for calcite {1014} structure.

Please obtain topology of calcite (1014) from prodrg and you can also see protein-ligand simulation protocol of gromacs exactly follow it. On Tue, Nov 12, 2019, 9:09 PM Hamid Zaree wrote: > Hi. > I would like to simulate Calcite structure in GROMACS. How could I make the > structure of Calcite

[gmx-users] segmentation fault core dumped

Greetings everyone I was following protein ligand complex tutorial. EM run was fine even with double precision. Steepest Descents converged to Fmax < 1000 in 101 steps Potential Energy = -2.71399964872904e+06 Maximum force = 9.15885947946535e+02 on atom 4411 Norm of force =

[gmx-users] (no subject)

greetings everyone I was following protein ligand complex tutorial. EM run was fine even with double precision. Steepest Descents converged to Fmax < 1000 in 101 steps Potential Energy = -2.71399964872904e+06 Maximum force = 9.15885947946535e+02 on atom 4411 Norm of force =

Re: [gmx-users] segmentation fault core dumped

First of all optimize the geometry of protein by using wincoot especially considering your respective atom/molecule/amino acid Change the algorithm of energy minimization to conjugate gradient If you can see the respective atom it is in collision with any other atom in any visualization tool. This