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Hi,
<br />
<br />My gromacs version is 4.0.5.
<br />I used grompp to generate tpr for 1ps simulation in this way
<br />grompp -f md1.mdp -n index.ndx  -p topol.top -c 0ps.gro  -t 0ps.trr -o 1ps.tpr
<br />mdrun -s 1ps.tpr -e 1ps.edr -o 1ps.trr -g 1ps.log -c 1ps.gro
<br />Here is my md1.mdp file:
<br />;
<br />title        = ttt
<br />cpp                 =  /lib/cpp
<br />constraints         =  hbonds
<br />;define              =  -DFLEX_SPC
<br />integrator          =  md
<br />emtol               =  100.0
<br />emstep              =  0.005
<br />dt                  =  0.002    ; ps !
<br />nsteps              =  500  ; total 1 ps
<br />nstcomm             =  500
<br />nstxout             =  500
<br />nstvout             =  500
<br />nstfout             =  500
<br />nstlog              =  500
<br />nstenergy           =  500
<br />nstlist             =  5
<br />ns_type             =  grid
<br />rlist               =  1.
<br />rcoulomb            =  1.
<br />rvdw                =  1.
<br />coulombtype         =  PME
<br />fourierspacing      =  0.12
<br />pme_order           =  4
<br />optimize_fft        =  yes
<br />Tcoupl              =  v-rescale
<br />tc-grps             =  A-chain B-chain drug SOL  NA+
<br />;tau_t               =  0.1  0.1
<br />tau_t               =  0.2  0.2 0.2 0.2 0.2
<br />ref_t               =  300.000000 300.000000 300.000000 300.000000 300.000000
<br />energygrps          =  A-chain B-chain drug SOL  NA+
<br />Pcoupl              =  berendsen
<br />Pcoupltype          =  isotropic
<br />;tau_p               =  0.1
<br />tau_p               =  0.25
<br />compressibility     =  5.4e-5
<br />ref_p               =  1.0
<br />gen_vel             =  yes
<br />gen_temp            =  300.000000
<br />gen_seed            =  173531
<br />
<br />--------------------------------------------------
<br />Then I execute below loop in other 59999 times for the totaly 60ns trajectories.
<br />grompp -f md2.mdp -n index.ndx  -p topol.top -c ${n-1}ps.gro  -t ${n-1}ps.trr -o ${n}ps.tpr
<br />
mdrun -s ${n}ps.tpr -e ${n}ps.edr -o ${n}ps.trr -g ${n}ps.log -c ${n}ps.gro
<br />The file md2.mdp is almost the same as md1.mdp but the parameter gen_vel=no.
<br />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.)
<br />
<br />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.
<br />The new method is:
<br />grompp -f md60ns.mdp -n index.ndx  -p topol.top -c 0ps.gro  -t 0ps.trr -o 60ns.tpr
<br />mpiexec -np 8 mdrun_mpi -s 60ns.tpr -e 60ns.edr -o 60ns.trr -g 60ns.log -c 60ns.gro
<br />The only different between md1.mdp and md60ns.mdp is nstep=30000000 in md60ns.mdp.
<br />
<br />Theses two data generated by different ways are totaly different.
<br />Here I mean different is not on the number buy mean the tendency of figure.
<br />In the movie of first method, protein runs violently and go outside the periodic boundary and then split by cubic edge.
<br />The interaction energy within protein also fluctuate in an unstable way.
<br />
<br />On the contrary, the second method generate a stable movie and fluctuation of interaction energy.
<br />Theotically these two should be the same, right?
<br />Is anything wrong in my work?
<br />
<br />Sincerely yours,
<br />Hsin-Lin
<br />
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