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SA error
- lianaliana
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13 years 11 months ago #367
by lianaliana
SA error was created by lianaliana
Heloo.
I tranformed a cg.gro into fg.gro using g_fg2cg and I'm now trying to run SA using fg.mdp (as in the tutorial), but the mdrun is finishing in error:
step 0
Program mdrun, VERSION 3.3.1
Source code file: nsgrid.c, line: 226
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 .. 729 ]
Please report this to the mailing list (This email address is being protected from spambots. You need JavaScript enabled to view it.)
Also, I opened my fg.gro in VMD, but I don't know how it's supposed to look, so I don't know if my input file has an error.
Can anybody help me?
Liana.
I tranformed a cg.gro into fg.gro using g_fg2cg and I'm now trying to run SA using fg.mdp (as in the tutorial), but the mdrun is finishing in error:
step 0
Program mdrun, VERSION 3.3.1
Source code file: nsgrid.c, line: 226
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 .. 729 ]
Please report this to the mailing list (This email address is being protected from spambots. You need JavaScript enabled to view it.)
Also, I opened my fg.gro in VMD, but I don't know how it's supposed to look, so I don't know if my input file has an error.
Can anybody help me?
Liana.
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- lianaliana
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13 years 11 months ago #368
by lianaliana
Replied by lianaliana on topic SA error
This is how my fg.gro looks like (vmd lines representation with some FG_W waters)
img6.imageshack.us/img6/7869/grofg.jpg
Thanks,
Liana.
img6.imageshack.us/img6/7869/grofg.jpg
Thanks,
Liana.
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- andrzej
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13 years 11 months ago #369
by andrzej
Replied by andrzej on topic SA error
This is starting frame ? Waters seems to be out of the box. Have You double chcecked amount of water molecules and protein atoms in the coarse grain gro file and the "starting" atomistic one ? What is Your mdp setup ? Can You send me mdp file ? This email address is being protected from spambots. You need JavaScript enabled to view it.
Andrzej
Andrzej
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- lianaliana
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13 years 11 months ago #370
by lianaliana
Replied by lianaliana on topic SA error
Hello
This is how the hole box looks like
img219.imageshack.us/img219/3540/grofgwaters.jpg
I hide waters before to be able to see the protein.
This is the fine grained structure obtained after CG simulations (input for SA).
My fg.mdp is the same as the tutorial one (I only changed the groups, since I don't have DPPC and I have NA+):
fg.mdp:
cpp = /lib/cpp
constraints = none
integrator = md
tinit = 0.0
dt = 0.002
nsteps = 40000
nstcomm = 0
nstxout = 10000
nstvout = 10000
nstfout = 10000
nstlog = 10000
nstenergy = 100
nstxtcout = 100
xtc_precision = 1000
nstlist = 10
energygrps = Protein NA+ 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 = Protein NA+ FG_W
ref_t = 320 320 320
tau_t = 0.1 0.1 0.1
Pcoupl = no
table_extension = 1.7
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 single single
annealing_npoints = 2 2 2
annealing_time = 0 60 0 60 0 60 ; CHANGE HERE -annealing control points for each group
annealing_temp = 1300 300 1300 300 400 300 ; list of temperatures at control points for each group
gen_vel = yes
gen_temp = 1300
gen_seed = 473529
lincs_warnangle = 100
I though the fg.gro structure looked strange because the atoms don't seem to be connected in the protein, is SA supposed to change that?
Both my fg.top and cg.top have the same number of waters
cg.top:
Protein 1
W 3079
NA+ 3
fg.top:
Protein 1
FG_W 3079
NA+ 3
Is there something wrong within my files?
Thank You,
Liana
This is how the hole box looks like
img219.imageshack.us/img219/3540/grofgwaters.jpg
I hide waters before to be able to see the protein.
This is the fine grained structure obtained after CG simulations (input for SA).
My fg.mdp is the same as the tutorial one (I only changed the groups, since I don't have DPPC and I have NA+):
fg.mdp:
cpp = /lib/cpp
constraints = none
integrator = md
tinit = 0.0
dt = 0.002
nsteps = 40000
nstcomm = 0
nstxout = 10000
nstvout = 10000
nstfout = 10000
nstlog = 10000
nstenergy = 100
nstxtcout = 100
xtc_precision = 1000
nstlist = 10
energygrps = Protein NA+ 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 = Protein NA+ FG_W
ref_t = 320 320 320
tau_t = 0.1 0.1 0.1
Pcoupl = no
table_extension = 1.7
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 single single
annealing_npoints = 2 2 2
annealing_time = 0 60 0 60 0 60 ; CHANGE HERE -annealing control points for each group
annealing_temp = 1300 300 1300 300 400 300 ; list of temperatures at control points for each group
gen_vel = yes
gen_temp = 1300
gen_seed = 473529
lincs_warnangle = 100
I though the fg.gro structure looked strange because the atoms don't seem to be connected in the protein, is SA supposed to change that?
Both my fg.top and cg.top have the same number of waters
cg.top:
Protein 1
W 3079
NA+ 3
fg.top:
Protein 1
FG_W 3079
NA+ 3
Is there something wrong within my files?
Thank You,
Liana
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- andrzej
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13 years 11 months ago #371
by andrzej
Replied by andrzej on topic SA error
Hey
There are couple of things You can check. First ions - how did You define mapping for ions ? If they are there only for neutralizing system, the easiest would be to remove them for SA ( or changing them for normal water bead - so 3 FG_W molecules more in fg.gro and 3 W in cg.gro file and the same in fg top file ) and then introduce them later with g_ion. Next You can try to play with parameters: cap_force decrease to 1000, decrease time step , decrease starting temperature, change integration to langevian dynamics (sd, to remove uneven temperature distribution), to see if the system can start ( use option -v for mdrun to see simulation progress ), and then you can go back to standard parametrs after identyfing the problem. Do You use constraints, if Yes change them to none.
Greetings
Andrzej
There are couple of things You can check. First ions - how did You define mapping for ions ? If they are there only for neutralizing system, the easiest would be to remove them for SA ( or changing them for normal water bead - so 3 FG_W molecules more in fg.gro and 3 W in cg.gro file and the same in fg top file ) and then introduce them later with g_ion. Next You can try to play with parameters: cap_force decrease to 1000, decrease time step , decrease starting temperature, change integration to langevian dynamics (sd, to remove uneven temperature distribution), to see if the system can start ( use option -v for mdrun to see simulation progress ), and then you can go back to standard parametrs after identyfing the problem. Do You use constraints, if Yes change them to none.
Greetings
Andrzej
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