Dear All,
I am doing simulation of an epoxy polymer and water system in gromacs using charmm27 forcefield. I got required temperature (300K) in NVT after 500 ps simulation and in NPT 30 ns simulation gave the density correctly but the pressure (1 atm) still now far. In both cases, polymer was relaxed while the water under position restraints. System contains 7000 atoms.
Am I on the right track of equilibration?
Thanks
Usually pressure fluctuation during NPT is more obvious than other parameters.So your system is well equilibrated when average of pressure results during equilibration phase is 1atm and other parameters (especially energy and RMSD) are Reasonable.
Best
Pressure has always too much error whether you are doing NVT or NPT and therefore sometimes difference comes in when you perform NVT and NPT. logically NVT or NPT should give you same thing if system is in equilibrium. Because you are looking for equilibiration, fluctuation and variation in volume rather than pressure should give you more appropriate idea. usually energy or temp converges more frequently and because in nvt you are keeping the volume constant, you are assuming your system is equilibrated but in NPT volume undergoes in changes where the difference comes in. Might this be the reason you are getting stable density after long time because your system volume wasn't stabilized before.
Thanks for your suggestions and discussions which help me to fix my problem.
I gree with collegues, however you must look too the size of the molecule to the time scale of equilibration.
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