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 = hbons
;define = -DFLEX_SPC  
integrator = md 
emtol = 100.0
emstep = 0.005 
dt = 0.002 ; ps!
nsteps = 500 ; total 1ps
nstcomm = 500  
ntsxout = 500  
ntsvout = 500 
ntsfout = 500  
ntslog = 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
rc-grps = A-chain B-chain drug SOL NA+
;tau_t = 0.1 0.1
tau_t =0.2 0.2 0.2 0.2
ref_t = 300.000000 300.000000 300.000000 300.00000 300.000000
energygrps = A-chain B-chain druhg 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
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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