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

[Hsin-Lin Chiang]

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+
;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
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.
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?
Is anything wrong in my work?

Sincerely yours,
Hsin-Lin
 
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