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
> 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
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
>
>
>
>
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,
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