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Hi, I am trying to equilibrate a membrane system made of DPPC, DUPC and cholesterol in 7:7:8 ratio in each leaflet . My system is crashing during NPT equilibration run with increased time step in order to stabilize the pressure in my system. the run fails with the warning that 1 or more water molecule could not be settled and followed by LINCS warnings and ultimately the run crashes.
could simulated annealing with custom temperature and pressure coupling groups be a possible solution for this problem ? if so what type of parameters should i use to conduct the annealing procedure ?
I am running all simulations using the GROMACS software package and i used the CHARMM GUI membrane builder module to assemble the input structure of the membrane and water. The charmm 36 parameter set for lipids was used.
any and all help, suggestions or guidance would be much appreciated.
thanks,
kamalika