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Reverse Transformation
- Rajat Desikan
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11 years 10 months ago #990
by Rajat Desikan
Reverse Transformation was created by Rajat Desikan
Hi All
I have a question. I needed to transform a martini protein to united atom atom so that I could compare the Ramachandran map of the simulated structure with the crystal structure. After I reverse mapped, I found some 140 residues in the prohibited region. So I just transformed a water box of martini waters back to spc waters. I noticed two things.
1) There are unusual bonds between atoms when I visualized the system in VMD. When I tried to energy minimize the reverse transformed structure, mdrun failed with the following error:
step 9: Water molecule starting at atom 8446 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)
2) I checked the energy of the reverse mapped water box at the end of simulated annealing. It came out to 5.3 e+5 at 300K. However, the energy of spc water at 300 K is -30 at 300K. Why does this discrepancy come about?
Thanks
I have a question. I needed to transform a martini protein to united atom atom so that I could compare the Ramachandran map of the simulated structure with the crystal structure. After I reverse mapped, I found some 140 residues in the prohibited region. So I just transformed a water box of martini waters back to spc waters. I noticed two things.
1) There are unusual bonds between atoms when I visualized the system in VMD. When I tried to energy minimize the reverse transformed structure, mdrun failed with the following error:
step 9: Water molecule starting at atom 8446 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)
2) I checked the energy of the reverse mapped water box at the end of simulated annealing. It came out to 5.3 e+5 at 300K. However, the energy of spc water at 300 K is -30 at 300K. Why does this discrepancy come about?
Thanks
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- djurre
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11 years 10 months ago #991
by djurre
Replied by djurre on topic Reverse Transformation
It sounds as if the systems doesn't get the time to fully relax after reverse transformation. Maybe you can try to do the reverse transformation slower (steps 7,8 and 9 of the tutorial). Or try to run a normal rev.trans. with more steps. Did you have a look at the systems energy? Did it reach a stable value during the rev. trans?
Also, I'm not sure if the ramachandran plots will tell you what you want. Since in Martini secondary structure is constrained, deviations in your plot will be much more the result of the atomistic forcefield or how good/bad the reverse transformation went.
Also, I'm not sure if the ramachandran plots will tell you what you want. Since in Martini secondary structure is constrained, deviations in your plot will be much more the result of the atomistic forcefield or how good/bad the reverse transformation went.
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- andrzej
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11 years 10 months ago #992
by andrzej
Replied by andrzej on topic Reverse Transformation
Hey,
Have you constrained the high energy dihedral angels of your protein to the values from a crystal structure (g_dihfix)
Can you post the reverse mdp parameters from mdp file that you use for the water system? (or better the whole mdp file). What ff you use ?
Andrzej
Have you constrained the high energy dihedral angels of your protein to the values from a crystal structure (g_dihfix)
Can you post the reverse mdp parameters from mdp file that you use for the water system? (or better the whole mdp file). What ff you use ?
Andrzej
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- Rajat Desikan
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11 years 10 months ago #993
by Rajat Desikan
Replied by Rajat Desikan on topic Reverse Transformation
@Andrez
I am not sure how to constrain the high energy dihedral angles of my protein to the values from the crystal structure. It was not there in the tutorial. Any help?
I am posting the mdp file for the water system:
cpp = /lib/cpp
constraints = none
integrator = md
tinit = 0.0
dt = 0.002
nsteps = 60000
nstcomm = 0
nstxout = 1000
nstvout = 1000
nstfout = 1000
nstlog = 1000
nstenergy = 100
nstxtcout = 100
xtc_precision = 1000
nstlist = 10
energygrps = FG_W
ns_type = grid
rlist = 0.9
coulombtype = Generalized-Reaction-Field
epsilon_rf = 62
rcoulomb = 1.5
rvdw = 1.0
Tcoupl = nose-hoover
tc-grps = FG_W
ref_t = 300
tau_t = 0.1
Pcoupl = no
table_extension = 1.2
dihre = simple ; Some dihedrals are restrained for instance peptide bonds are set to trans conformation.
dihre_fc = 500
dihre_tau = 0.0
nstdihreout = 50
cap_force = 15000
cap_a = 100
fc_restr = 12000
r_CGW = 0.21
fc_restrW = 400
rel_steps = 0
rel_water = no
andersen_seed = 815131
annealing = single
annealing_npoints = 2
annealing_time = 0 100 ; CHANGE HERE -annealing control points for each group
annealing_temp = 1300 300 ; list of temperatures at control points for each group
@Djurre, I have done the rev transformation according to step 9 (highest number of steps)...
the systems did reach a stable energy, but much higher than the fully atomistic runs.
I am transforming everything into the ffG43a2 forcefield. Is that a problem?
Thanks for all the help. Much appreciated.:)
I am not sure how to constrain the high energy dihedral angles of my protein to the values from the crystal structure. It was not there in the tutorial. Any help?
I am posting the mdp file for the water system:
cpp = /lib/cpp
constraints = none
integrator = md
tinit = 0.0
dt = 0.002
nsteps = 60000
nstcomm = 0
nstxout = 1000
nstvout = 1000
nstfout = 1000
nstlog = 1000
nstenergy = 100
nstxtcout = 100
xtc_precision = 1000
nstlist = 10
energygrps = FG_W
ns_type = grid
rlist = 0.9
coulombtype = Generalized-Reaction-Field
epsilon_rf = 62
rcoulomb = 1.5
rvdw = 1.0
Tcoupl = nose-hoover
tc-grps = FG_W
ref_t = 300
tau_t = 0.1
Pcoupl = no
table_extension = 1.2
dihre = simple ; Some dihedrals are restrained for instance peptide bonds are set to trans conformation.
dihre_fc = 500
dihre_tau = 0.0
nstdihreout = 50
cap_force = 15000
cap_a = 100
fc_restr = 12000
r_CGW = 0.21
fc_restrW = 400
rel_steps = 0
rel_water = no
andersen_seed = 815131
annealing = single
annealing_npoints = 2
annealing_time = 0 100 ; CHANGE HERE -annealing control points for each group
annealing_temp = 1300 300 ; list of temperatures at control points for each group
@Djurre, I have done the rev transformation according to step 9 (highest number of steps)...
the systems did reach a stable energy, but much higher than the fully atomistic runs.
I am transforming everything into the ffG43a2 forcefield. Is that a problem?
Thanks for all the help. Much appreciated.:)
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- Rajat Desikan
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11 years 10 months ago #1006
by Rajat Desikan
Replied by Rajat Desikan on topic Reverse Transformation
Hi Guys,
I am stuck and would appreciate a reply.
Thanks
I am stuck and would appreciate a reply.
Thanks
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11 years 10 months ago #1007
by Rajat Desikan
Replied by Rajat Desikan on topic Reverse Transformation
I ran a united atom SPC waterbox at 300 K. I got the potential energy as -30 KJ/mol....I am getting around -150 KJ/mol for the reverse transformed waterbox.!
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- andrzej
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11 years 10 months ago #1008
by andrzej
Replied by andrzej on topic Reverse Transformation
Hey, to constrain certain dihedrals you can use g_dihfix (what it does and how to use it is described in the reconstruction publication).
So after the sim annealing run you obtain energies about -150, whereas from standard atomistic run energies are on magnitude -30 kJ/mol ? It would mean that the water system reached some local energy minimum after the reverse procedure. Are there any artifacts in the system ?
Andrzej
So after the sim annealing run you obtain energies about -150, whereas from standard atomistic run energies are on magnitude -30 kJ/mol ? It would mean that the water system reached some local energy minimum after the reverse procedure. Are there any artifacts in the system ?
Andrzej
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- Rajat Desikan
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11 years 10 months ago #1009
by Rajat Desikan
Replied by Rajat Desikan on topic Reverse Transformation
Hi Andrez.
I checked the system in VMD. There do not seem to be any artifacts. I could not make out any unusual bonds, etc. Can I send you the reverse mapped water.gro file?
I figured out the use of g_dihfix. Thanks :)
I checked the system in VMD. There do not seem to be any artifacts. I could not make out any unusual bonds, etc. Can I send you the reverse mapped water.gro file?
I figured out the use of g_dihfix. Thanks :)
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- andrzej
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11 years 10 months ago #1021
by andrzej
Replied by andrzej on topic Reverse Transformation
Hey,
If the energy of the transformed system is lower than of a reference water system (as you report) and there are no clashes, then the procedure finished successfully. You can additionally monitor rdf or the evolution of the system when a standard simulation is again started.
Andrzej
If the energy of the transformed system is lower than of a reference water system (as you report) and there are no clashes, then the procedure finished successfully. You can additionally monitor rdf or the evolution of the system when a standard simulation is again started.
Andrzej
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- Rajat Desikan
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11 years 10 months ago #1023
by Rajat Desikan
Replied by Rajat Desikan on topic Reverse Transformation
Hi Andrzej, thanks for the reply
But the energy is 5 times more negative than a spc waterbox equilibrated to the same parameters. Is it not fallacious? If I were benchmarking reverse mapping based on energy, I would think that something has gone wrong.
But the energy is 5 times more negative than a spc waterbox equilibrated to the same parameters. Is it not fallacious? If I were benchmarking reverse mapping based on energy, I would think that something has gone wrong.
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- andrzej
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11 years 10 months ago #1024
by andrzej
Replied by andrzej on topic Reverse Transformation
Hey,
In general energies from the reverse transformation are lower, since a systems goes to some allowed local minimum. In the 'normal' simulation you average over many different frames, with different energies. Here you reconstruct just one CG frame. What is the distribution around the AA average that you report?
In general energies from the reverse transformation are lower, since a systems goes to some allowed local minimum. In the 'normal' simulation you average over many different frames, with different energies. Here you reconstruct just one CG frame. What is the distribution around the AA average that you report?
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- Rajat Desikan
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11 years 10 months ago #1026
by Rajat Desikan
Replied by Rajat Desikan on topic Reverse Transformation
Hi All
I figured out the issue. Thanks for all the help :)
I figured out the issue. Thanks for all the help :)
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