[gmx-users] different output generated by continue and discontinue simulation

[Mark Abraham]

On 12/16/10, Hsin-Lin Chiang  <jiangsl at phys.sinica.edu.tw> wrote:
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> Hi,
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> 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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> 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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This is bad - see http://www.gromacs.org/Documentation/Terminology/Thermostats

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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
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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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You are following neither of the approaches recommended here http://www.gromacs.org/Documentation/How-tos/Doing_Restarts


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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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> 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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See http://www.gromacs.org/Documentation/Terminology/Reproducibility


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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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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

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> Is anything wrong in my work?
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> Sincerely yours,
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> Hsin-Lin
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