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