[gmx-users] different output generated by continue and discontinue simulation
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#160; -p topol.top -c 0ps.gro#160; -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#160;#160;#160;#160;#160;#160;#160; = ttt
cpp#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; /lib/cpp
constraints#160;#160;#160;#160;#160;#160;#160;#160; =#160; hbonds
;define#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; -DFLEX_SPC
integrator#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; md
emtol#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 100.0
emstep#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 0.005
dt#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 0.002#160;#160;#160; ; ps !
nsteps#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 500#160; ; total 1 ps
nstcomm#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 500
nstxout#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 500
nstvout#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 500
nstfout#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 500
nstlog#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 500
nstenergy#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160;
500
nstlist#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 5
ns_type#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; grid
rlist#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 1.
rcoulomb#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 1.
rvdw#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 1.
coulombtype#160;#160;#160;#160;#160;#160;#160;#160; =#160; PME
fourierspacing#160;#160;#160;#160;#160; =#160; 0.12
pme_order#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 4
optimize_fft#160;#160;#160;#160;#160;#160;#160; =#160; yes
Tcoupl#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; v-rescale
tc-grps#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; A-chain B-chain drug SOL#160; NA+
;tau_t#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 0.1#160; 0.1
tau_t#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 0.2#160; 0.2 0.2 0.2 0.2
ref_t#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 300.00 300.00 300.00 300.00 300.00
energygrps#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160;
A-chain B-chain drug SOL#160; NA+
Pcoupl#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; berendsen
Pcoupltype#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160;
isotropic
;tau_p#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 0.1
tau_p#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 0.25
compressibility#160;#160;#160;#160; =#160; 5.4e-5
ref_p#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 1.0
gen_vel#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; yes
gen_temp#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 300.00
gen_seed#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 173531
--
Then I execute below loop in other 5 times for the totaly 60ns trajectories.
grompp -f md2.mdp -n index.ndx#160; -p topol.top -c ${n-1}ps.gro#160; -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#160; -p topol.top -c 0ps.gro#160; -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=3000 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
[gmx-users] different output generated by continue and discontinue simulation
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#160; -p topol.top -c 0ps.gro#160; -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#160;#160;#160;#160;#160;#160;#160; = ttt
cpp#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; /lib/cpp
constraints#160;#160;#160;#160;#160;#160;#160;#160; =#160; hbonds
;define#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; -DFLEX_SPC
integrator#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; md
emtol#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 100.0
emstep#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 0.005
dt#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 0.002#160;#160;#160; ; ps !
nsteps#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 500#160; ; total 1 ps
nstcomm#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 500
nstxout#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 500
nstvout#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 500
nstfout#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 500
nstlog#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 500
nstenergy#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160;
500
nstlist#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 5
ns_type#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; grid
rlist#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 1.
rcoulomb#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 1.
rvdw#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 1.
coulombtype#160;#160;#160;#160;#160;#160;#160;#160; =#160; PME
fourierspacing#160;#160;#160;#160;#160; =#160; 0.12
pme_order#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 4
optimize_fft#160;#160;#160;#160;#160;#160;#160; =#160; yes
Tcoupl#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; v-rescale
tc-grps#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; A-chain B-chain drug SOL#160; NA+
;tau_t#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 0.1#160; 0.1
tau_t#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 0.2#160; 0.2 0.2 0.2 0.2
ref_t#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 300.00 300.00 300.00 300.00 300.00
energygrps#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160;
A-chain B-chain drug SOL#160; NA+
Pcoupl#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; berendsen
Pcoupltype#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160;
isotropic
;tau_p#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 0.1
tau_p#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 0.25
compressibility#160;#160;#160;#160; =#160; 5.4e-5
ref_p#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 1.0
gen_vel#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; yes
gen_temp#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 300.00
gen_seed#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 173531
--
Then I execute below loop in other 5 times for the totaly 60ns
trajectories.
grompp -f md2.mdp -n index.ndx#160; -p topol.top -c ${n-1}ps.gro#160; -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#160; -p topol.top -c 0ps.gro#160; -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=3000 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
[gmx-users] different output generated by continue and discontinue simulation
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#160; -p topol.top -c 0ps.gro#160; -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 #160;
constraints = hbons
;define = -DFLEX_SPC #160;
integrator = md#160;
emtol = 100.0
emstep = 0.005#160;
dt = 0.002 ; ps!
nsteps = 500 ; total 1ps
nstcomm = 500 #160;
ntsxout = 500 #160;
ntsvout = 500#160;
ntsfout = 500 #160;
ntslog = 500#160;
nstenergy = 500
nstlist = 5#160; #160;
ns_type = grid #160;
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 = 300.00 300.00 300.00 300.0 300.00
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 = 300.00
gen_seed = 173531
gen_seed#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 173531
--
Then I execute below loop in other 5 times for the totaly 60ns
trajectories.
grompp -f md2.mdp -n index.ndx#160; -p topol.top -c ${n-1}ps.gro#160; -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#160; -p topol.top -c 0ps.gro#160; -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=3000 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
--- End of Forwarded Message ---
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[gmx-users] different output generated by continue and discontinue simulation
Hi, Mark
tc-grps#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; A-chain B-chain drug SOL#160; NA+
This is bad - see http://www.gromacs.org/Documentation/Terminology/Thermostats
Thank you for your website.#160; I understand now.
grompp -f md2.mdp -n index.ndx#160; -p topol.top -c ${n-1}ps.gro#160; -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
You are following neither of the approaches recommended here
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts
Ya, I'm sorry but my colleborator give me that before.
It is similiar to the commends connect position restrained dynamics and MD.
You can find grompp read gro and trr of last time frame to make a tpr file of
next time frame.
I thought this cause the time write on each snapshot is 0, but the dynamics is
still processing.
Did I miss something?
You say the pressure-coupling will be lost in each ps, does it mean that trr
file doesn't have this message inside?
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.
See http://www.gromacs.org/Documentation/Terminology/Reproducibility
Ya, I know this since last time you show me this web in mailing list.
Thank you again.
But the different between these two outputs is totaly different.
I have four systems with different parameter gen_seed.
First is always unstable and irregular, but second is stable and regular.
On the contrary, the second method generate a stable movie and fluctuation
of interaction energy.
Theotically these two should be the same, right?
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
Sorry I don't understand you here.
Do you mean second way seems to more correct?
And what kind of mutual convergence you mean here?
Does It mean I can try to find mutual convergence in output of second way?
I'm sorry for my stupid and poor English.
Sincerely yours,
Hsin-Lin
--
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Please search the archive at
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Re: [gmx-users] different output generated by continue and discontinue simulation
Hsin-Lin Chiang wrote:
Hi, Mark
tc-grps = A-chain B-chain drug SOL NA+
This is bad - see
http://www.gromacs.org/Documentation/Terminology/Thermostats
Thank you for your website. I understand now.
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
You are following neither of the approaches recommended here
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts
Ya, I'm sorry but my colleborator give me that before.
It is similiar to the commends connect position restrained dynamics and MD.
You can find grompp read gro and trr of last time frame to make a tpr
file of next time frame.
I thought this cause the time write on each snapshot is 0, but the
dynamics is still processing.
Did I miss something?
You say the pressure-coupling will be lost in each ps, does it mean that
trr file doesn't have this message inside?
Pressure coupling information is stored in the .edr file. If you don't pass it
to grompp, you lose it. The better method is to use a checkpoint (.cpt) file,
which contains everything necessary to accurately continue the simulation.
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.
See http://www.gromacs.org/Documentation/Terminology/Reproducibility
Ya, I know this since last time you show me this web in mailing list.
Thank you again.
But the different between these two outputs is totaly different.
I have four systems with different parameter gen_seed.
First is always unstable and irregular, but second is stable and regular.
It sounds like you have an unstable system, that, under certain favorable
conditions, seems to work, but in other cases, doesn't. I'd investigate why the
first system is failing, since it probably really is a problem in all of them.
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
On the contrary, the second method generate a stable movie and
fluctuation of interaction energy.
Theotically these two should be the same, right?
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
Sorry I don't understand you here.
Do you mean second way seems to more correct?
Not correct, but rather not yet suffering from the same problem.
And what kind of mutual convergence you mean here?
Systems only converge reliably over long time periods, i.e. in theory,
independent observations can only be reliably obtained over sufficient time.
-Justin
Does It mean I can try to find mutual convergence in output of second way?
I'm sorry for my stupid and poor English.
Sincerely yours,
Hsin-Lin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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