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

[Hsin-Lin Chiang]

Sorry for the abnormal code. 
I have fixed that.
---
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 fordouble 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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