On 12/16/10, Hsin-Lin Chiang <jian...@phys.sinica.edu.tw> wrote: > > > > > > > > > > Hi, > > > > My gromacs version is 4.0.5. > > I used grompp to generate tpr for 1ps simulation in this way > > grompp -f md1.mdp -n index.ndx -p topol.top -c 0ps.gro -t 0ps.trr -o 1ps.tpr > > mdrun -s 1ps.tpr -e 1ps.edr -o 1ps.trr -g 1ps.log -c 1ps.gro > > Here is my md1.mdp file: > > ; > > title = ttt > > cpp = /lib/cpp > > constraints = hbonds > > ;define = -DFLEX_SPC > > integrator = md > > emtol = 100.0 > > emstep = 0.005 > > dt = 0.002 ; ps ! > > nsteps = 500 ; total 1 ps > > nstcomm = 500 > > nstxout = 500 > > nstvout = 500 > > nstfout = 500 > > nstlog = 500 > > nstenergy = 500 > > nstlist = 5 > > ns_type = grid > > rlist = 1. > > rcoulomb = 1. > > rvdw = 1. > > coulombtype = PME > > fourierspacing = 0.12 > > pme_order = 4 > > optimize_fft = yes > > > > > >
> > > > > Tcoupl = v-rescale > > tc-grps = A-chain B-chain drug SOL NA+ > > > > > This is bad - see http://www.gromacs.org/Documentation/Terminology/Thermostats > > > > > > ;tau_t = 0.1 0.1 > > tau_t = 0.2 0.2 0.2 0.2 0.2 > > ref_t = 300.000000 300.000000 300.000000 300.000000 300.000000 > > energygrps = A-chain B-chain drug SOL NA+ > > Pcoupl = berendsen > > Pcoupltype = isotropic > > ;tau_p = 0.1 > > tau_p = 0.25 > > compressibility = 5.4e-5 > > ref_p = 1.0 > > gen_vel = yes > > gen_temp = 300.000000 > > gen_seed = 173531 > > > > -------------------------------------------------- > > Then I execute below loop in other 59999 times for the totaly 60ns > trajectories. > > grompp -f md2.mdp -n index.ndx -p topol.top -c ${n-1}ps.gro -t ${n-1}ps.trr > -o ${n}ps.tpr > > > mdrun -s ${n}ps.tpr -e ${n}ps.edr -o ${n}ps.trr -g ${n}ps.log -c ${n}ps.gro > > > > > You are following neither of the approaches recommended here http://www.gromacs.org/Documentation/How-tos/Doing_Restarts > > > > > The file md2.mdp is almost the same as md1.mdp but the parameter gen_vel=no. > > Here ${n-1}ps.gro and ${n-1}.trr mean I use last time frame trajectory to > continue.(I didn't really use this commend $(n-1) in bash script, it won't > work.) > > > > I change the other way to run parallel simulation on the same system for > double check since above script is difficult to parallelize in public > computer. > > The new method is: > > grompp -f md60ns.mdp -n index.ndx -p topol.top -c 0ps.gro -t 0ps.trr -o > 60ns.tpr > > mpiexec -np 8 mdrun_mpi -s 60ns.tpr -e 60ns.edr -o 60ns.trr -g 60ns.log -c > 60ns.gro > > The only different between md1.mdp and md60ns.mdp is nstep=30000000 in > md60ns.mdp. > > > > Theses two data generated by different ways are totaly different. > > Here I mean different is not on the number buy mean the tendency of figure. > > > > > See http://www.gromacs.org/Documentation/Terminology/Reproducibility > > > > > > In the movie of first method, protein runs violently and go outside the > periodic boundary and then split by cubic edge. > > The interaction energy within protein also fluctuate in an unstable way. > > > > On the contrary, the second method generate a stable movie and fluctuation of > interaction energy. > > Theotically these two should be the same, right? > > > > > The second is probably happier about not losing the pressure-coupling information every 1ns. However only much much longer trajectories should show mutual convergence, and the movie is not a reasonable way to look for it. Mark > > > > > > Is anything wrong in my work? > > > > Sincerely yours, > > Hsin-Lin > > > > > > > > > > > >
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