[gmx-users] Please answer this!!!
nimavaeesa at yahoo.com
Sun Jul 12 10:38:29 CEST 2015
Hi, Dear users,I have created a box of polymer with about 50 molecules. I'm performing NPT runs to reach to the pressure of 1 bar. After a long time of simulation (15 ns) the average pressure is still about -0.5 and the density has saturated to around 700 kg/m^3 which should become 1200 kg/m^3 at the pressure of one bar. These are the related parameters in .mdp file:
; Pressure coupling is onpcoupl = berendsen ; Pressure coupling on in NPTpcoupltype = isotropic ; uniform scaling of box vectorstau_p = 0.2 ; time constant, in psref_p = 1.0 ; reference pressure, in barcompressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
Does anyone know how can I fix this? Which parameters should I change to reach the desired pressure and density?Thanks in advance.-Nima Azar
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