Re: [gmx-users] Simulation crashed, fatal error: Bond length not finite and warning: Pressure scaling more than 1%.

Dear all, Thank you for your suggestions and help. @Quyen, I checked the energies, box fluctuations and pressure deviations and everything seem correct: Energies (potential, kinetic and total) were stable during the simulation and the average of the pressure was 1.04 bar. @ Peter, I

Re: [gmx-users] Simulation crashed, fatal error: Bond length not finite and warning: Pressure scaling more than 1%.

> You equilibrations are probably too short. There are some pretty slow > processes in lipid membranes. The original poster stated that the system crashed after microseconds of simulation, so this is not the case. The pressure fluctuation message could be a red herring, with a system explosion

Re: [gmx-users] Simulation crashed, fatal error: Bond length not finite and warning: Pressure scaling more than 1%.

You equilibrations are probably too short. There are some pretty slow processes in lipid membranes. Peter On Fri, May 25, 2018 at 6:00 PM, Quyen V. Vu wrote: > Hi Zeined, > Have you check the energy , the box fluctuations and pressure deviations ? > Best, > Quyen > > > >

Re: [gmx-users] Simulation crashed, fatal error: Bond length not finite and warning: Pressure scaling more than 1%.

Hi Zeined, Have you check the energy , the box fluctuations and pressure deviations ? Best, Quyen On Fri, May 25, 2018 at 6:30 PM, zeineb SI CHAIB wrote: > Dear GMX users, > > > I'm running a coarse-grained simulation of a homo-dimer in a membrane > composed of POPC,

[gmx-users] Simulation crashed, fatal error: Bond length not finite and warning: Pressure scaling more than 1%.

Dear GMX users, I'm running a coarse-grained simulation of a homo-dimer in a membrane composed of POPC, POPE, and CHOL (31%, 41%, 28% respectively), using MARTINI force field and GROMACS software. I followed the usual steps with 1ns minimization, 50 ns NVT equilibration followed by 50ns NPT