Hi all,
I have something here which I am would like to pick your brains. Thank you in advance. In my trial-and-error attempt to equilibrate my membrane protein system, I encountered this problem. I was playing with 2 different mdp files (in succession), first by using the Nose Hoover then v-rescale. I realised upon changing from the former to the latter there was a drop in simulation temperature from 310K to about 263K. Not sure if this have anything to do with the switch of thermostat or due to some other parameter change? The mdp file below which contain the Nose Hoover thermostat was used to generate A3_1posre (see below grompp command) title = NPT define = -DPOSRES ; Run parameters integrator = md nsteps = 500000 ; 2 * 500000 = 1000 ps (1 ns) dt = 0.002 ; Output control nstxout = 50000 nstvout = 50000 nstenergy = 500 nstlog = 500 ; Bond parameters continuation = yes constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ; Neighborsearching ns_type = grid nstlist = 5 rlist = 1.2 rcoulomb = 1.2 rvdw = 1.2 ; Electrostatics coulombtype = PME pme_order = 4 fourierspacing = 0.16 ; Temperature coupling is on tcoupl = Nose-Hoover tc-grps = Protein POPC SOL_CL- tau_t = 0.1 0.1 0.1 ref_t = 310 310 310 ; Pressure coupling is on pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 ref_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 ; Periodic boundary conditions pbc = xyz ; Dispersion correction DispCorr = EnerPres ; Velocity generation gen_vel = no ; COM motion removal nstcomm = 1 comm-mode = Linear comm-grps = Protein_POPC SOL_CL- ; Energy groups energygrps = Protein POPC SOL_CL- I then use another mdp file containing v-rescale thermostat to extend the simulation grompp -f v-rescale.mdp -c A3_1posre.gro -o A3_noposre.tpr -n index.ndx -p topol_3.top mdrun_mpi -s A3_noposre.tpr -v -cpi A3_1posre.cpt title = NPT define = ; Run parameters integrator = md nsteps = 1000000 ; 2 * 1000000 = 2000 ps (2 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 250000 nstvout = 250000 nstenergy = 1000 nstlog = 500 nstxtcout = 250000 ; Bond parameters continuation = yes constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ; Neighborsearching ns_type = grid nstlist = 10 rlist = 1.2 rcoulomb = 1.2 rvdw = 1.2 ; Electrostatics coulombtype = PME pme_order = 4 fourierspacing = 0.12 ; Temperature coupling is on tcoupl = v-rescale fluctuation tc-grps = Protein POPC SOL_CL- tau_t = 0.1 0.1 0.1 ref_t = 310 310 310 ; Pressure coupling is on pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 1.0 ref_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; Velocity generation gen_vel = no ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_POPC SOL_CL- ; Energy groups energygrps = Protein POPC SOL_CL- << This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK & Malaysia legislation. >>
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