Dear Users Dr. Micholas : Do you suggest that I do a longer run ? I am doing another NPT carrying on from the previous NPT with a Parrinello-Rahman barostat. I am attaching the NPT pressure and density plots , if anyone wants to have a look at them.
Dr. Vitaly : I was thinking that my equilibration did not reach the reference pressure because I need to do a longer run. Tsjerk Wassenaar : Are you hinting at the running average for my pressure plot ? I did not plot that. I was thinking of running a much longer simulation and use a different barostat for another NPT simulation. Dan Sponseller : I am also thinking of a much longer simulation using small nstenergy value. My present value is 100. To all : If you have any comment then please share. My previous mail as reference : Dear Users I have a DNA-Protein system and I use AMBER99SB-Parmbsc0 ff in GROMACS 4.5.7 single precision. I use spc216 for solvation and TIP 3P water model. My earlier work flow 1) Topology preparation 2) Box , Solvation and Ions 3) Energy minimization - Steepest descent ( converged after 1291 steps ) 4) NVT equilibration using a V-rescale thermostat and ref temp = 300 K average temp = 299.7 K after 100 ps NVT sim. Total energy also constant with minimal error. 5) Next is NPT sim ( with same thermostat on ) *Pressure Coupling part of npt.mdp file :* ; Pressure coupling is on pcoupl = Berendsen ; Pressure coupling on in NPT, also weak coupling pcoupltype = isotropic ; uniform scaling of x-y-z box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure (in bar) compressibility = 4.5e-5 ; isothermal compressibility, bar^-1 refcoord_scaling = com *g_energy output of npt.edr :* A)​Statistics over 50001 steps [ 0.0000 through 100.0000 ps ], 1 data sets All statistics are over 10001 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------ ------------------------------------------------- Pressure -5.5706 6.2 84.8085 38.1219 (bar) (B)All statistics are over 10001 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------ ------------------------------------------------- Density 1012.13 0.55 1.87172 3.17412 (kg/m^3) *My run parameters are :* ; Run parameters integrator = md ; leap-frog integrator nsteps = 50000 ; 2 * 50000 = 100 ps dt = 0.002 ; 2 fs My reference pressure is 1 bar , the average pressure is -5.5 bar . I believe that the system failed to achieve the reference set pressure. *So should I carry out the simulation for a longer time ?? Or should I use a different barostat on the next NPT run or do it in a fresh NPT run.* *Kindly suggest.* Thanks & Regards Agnivo Gosai Grad Student, Iowa State University.
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