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Error during nvt equilibration
- anuvc84
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Topic Author
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11 years 2 months ago #1407
by anuvc84
Error during nvt equilibration was created by anuvc84
Dear users,
I am trying to do a simulation of protein in water using gromacs 4.5.3 with martini22.When I tried to do nvt equilibration using mdrun command,
It showed following error
"Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated"
There were LINCS warning also before this error.During energy minimization also, there were a few lincs warning in the beginning after which it ran fine.
The mdp file used is as shown below:
define = -DPOSRES
integrator = md
tinit = 0.0
dt = 0.02
nsteps = 50000
nstcomm = 1
comm-grps =
nstxout = 5000
nstvout = 5000
nstfout = 0
nstlog = 1000
nstenergy = 100
nstxtcout = 1000
xtc_precision = 100
xtc-grps =
energygrps = Protein W
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = Berendsen
tc-grps = System
tau_t = 1.0
ref_t = 300
gen_vel = yes
gen_temp = 300
gen_seed = 473529
constraints = all-bonds
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
Can anybody please help me on how to go about with this?
Thank You,
with regards,
Anu
I am trying to do a simulation of protein in water using gromacs 4.5.3 with martini22.When I tried to do nvt equilibration using mdrun command,
It showed following error
"Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated"
There were LINCS warning also before this error.During energy minimization also, there were a few lincs warning in the beginning after which it ran fine.
The mdp file used is as shown below:
define = -DPOSRES
integrator = md
tinit = 0.0
dt = 0.02
nsteps = 50000
nstcomm = 1
comm-grps =
nstxout = 5000
nstvout = 5000
nstfout = 0
nstlog = 1000
nstenergy = 100
nstxtcout = 1000
xtc_precision = 100
xtc-grps =
energygrps = Protein W
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = Berendsen
tc-grps = System
tau_t = 1.0
ref_t = 300
gen_vel = yes
gen_temp = 300
gen_seed = 473529
constraints = all-bonds
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
Can anybody please help me on how to go about with this?
Thank You,
with regards,
Anu
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- xavier
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11 years 1 month ago #1441
by xavier
Replied by xavier on topic Error during nvt equilibration
It is not clear what can be our problem! Did you solve it?
Did you minimize? What kind of position restrain you use?
Did you minimize? What kind of position restrain you use?
anuvc84 wrote: Dear users,
I am trying to do a simulation of protein in water using gromacs 4.5.3 with martini22.When I tried to do nvt equilibration using mdrun command,
It showed following error
"Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated"
There were LINCS warning also before this error.During energy minimization also, there were a few lincs warning in the beginning after which it ran fine.
The mdp file used is as shown below:
define = -DPOSRES
integrator = md
tinit = 0.0
dt = 0.02
nsteps = 50000
nstcomm = 1
comm-grps =
nstxout = 5000
nstvout = 5000
nstfout = 0
nstlog = 1000
nstenergy = 100
nstxtcout = 1000
xtc_precision = 100
xtc-grps =
energygrps = Protein W
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = Berendsen
tc-grps = System
tau_t = 1.0
ref_t = 300
gen_vel = yes
gen_temp = 300
gen_seed = 473529
constraints = all-bonds
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
Can anybody please help me on how to go about with this?
Thank You,
with regards,
Anu
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- anuvc84
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Topic Author
- Visitor
11 years 1 month ago #1444
by anuvc84
Replied by anuvc84 on topic Error during nvt equilibration
Sir,
Thank you for the reply.
I could run nvt equilibration using gromacs-4.6 version with the following mdp file.
define = -DPOSRES
title = Martini
integrator = md
dt = 0.01
nsteps = 50000
nstcomm = 10
comm-grps =
nstxout = 100
nstvout = 100
nstfout = 100
nstlog = 1000
nstenergy = 100
nstxtcout = 1000
xtc_precision = 100
xtc-grps = Protein
energygrps = Protein
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
tcoupl = v-rescale
tc-grps = System
tau_t = 1.0
ref_t = 300
gen_vel = yes
gen_temp = 300
gen_seed = 473529
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
and for NPT equilibration,following lines were added to the mdp file mentioned above
Pcoupltype = isotropic
tau_p = 5.0
compressibility = 3e-4
ref_p = 1.0
refcoord-scaling = com
The simulation ran without any warning or errors, but I have two doubts:
1.For temperature coupling, is it right to use
"tc-grps = System" rather than coupling individual groups ("tc_grps= Protein W NA")?
2.During NVT and NPT equilibration, do i need to change the "constraints" option in the mdp file.Currently I used "constraints=none"
Thank You,
with regards
Anu
Thank you for the reply.
I could run nvt equilibration using gromacs-4.6 version with the following mdp file.
define = -DPOSRES
title = Martini
integrator = md
dt = 0.01
nsteps = 50000
nstcomm = 10
comm-grps =
nstxout = 100
nstvout = 100
nstfout = 100
nstlog = 1000
nstenergy = 100
nstxtcout = 1000
xtc_precision = 100
xtc-grps = Protein
energygrps = Protein
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
tcoupl = v-rescale
tc-grps = System
tau_t = 1.0
ref_t = 300
gen_vel = yes
gen_temp = 300
gen_seed = 473529
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
and for NPT equilibration,following lines were added to the mdp file mentioned above
Pcoupltype = isotropic
tau_p = 5.0
compressibility = 3e-4
ref_p = 1.0
refcoord-scaling = com
The simulation ran without any warning or errors, but I have two doubts:
1.For temperature coupling, is it right to use
"tc-grps = System" rather than coupling individual groups ("tc_grps= Protein W NA")?
2.During NVT and NPT equilibration, do i need to change the "constraints" option in the mdp file.Currently I used "constraints=none"
Thank You,
with regards
Anu
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- xavier
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11 years 1 month ago #1446
by xavier
Sounds good.
I would suggest that you couple the protein and the solvent separately but including the NA to the W group.
constraints should stay none. They are explicitly defined in the topologies of the proteins.
Replied by xavier on topic Error during nvt equilibration
anuvc84 wrote: Sir,
Thank you for the reply.
I could run nvt equilibration using gromacs-4.6 version with the following mdp file.
define = -DPOSRES
title = Martini
integrator = md
dt = 0.01
nsteps = 50000
nstcomm = 10
comm-grps =
nstxout = 100
nstvout = 100
nstfout = 100
nstlog = 1000
nstenergy = 100
nstxtcout = 1000
xtc_precision = 100
xtc-grps = Protein
energygrps = Protein
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
tcoupl = v-rescale
tc-grps = System
tau_t = 1.0
ref_t = 300
gen_vel = yes
gen_temp = 300
gen_seed = 473529
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
and for NPT equilibration,following lines were added to the mdp file mentioned above
Pcoupltype = isotropic
tau_p = 5.0
compressibility = 3e-4
ref_p = 1.0
refcoord-scaling = com
The simulation ran without any warning or errors, but I have two doubts:
1.For temperature coupling, is it right to use
"tc-grps = System" rather than coupling individual groups ("tc_grps= Protein W NA")?
2.During NVT and NPT equilibration, do i need to change the "constraints" option in the mdp file.Currently I used "constraints=none"
Thank You,
with regards
Anu
Sounds good.
I would suggest that you couple the protein and the solvent separately but including the NA to the W group.
constraints should stay none. They are explicitly defined in the topologies of the proteins.
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- anuvc84
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Topic Author
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11 years 1 month ago #1457
by anuvc84
Replied by anuvc84 on topic Error during nvt equilibration
Dear users,
When I ran g_rms to calculate the rmsd with respect to the starting structure (for 500ns simulation of an octamer using gromacs-4.6 with martini22 force field). I could see some sharp jumps in rmsd (from 1.0A to 5.5A) at various time points in the trajectory.I would like to know whether anybody has faced this kind of problem and also how to go about with it?
Thank you,
with regards,
Anu
When I ran g_rms to calculate the rmsd with respect to the starting structure (for 500ns simulation of an octamer using gromacs-4.6 with martini22 force field). I could see some sharp jumps in rmsd (from 1.0A to 5.5A) at various time points in the trajectory.I would like to know whether anybody has faced this kind of problem and also how to go about with it?
Thank you,
with regards,
Anu
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- xavier
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11 years 1 month ago #1458
by xavier
Replied by xavier on topic Error during nvt equilibration
Your system is probably going over the boundary periodic conditions. You have to treat your trajectory prior the g_rms using trjconv and playing with the pbc options: nojump, fitting, mol ... it is a bit tricky the first time but it works :))
anuvc84 wrote: Dear users,
When I ran g_rms to calculate the rmsd with respect to the starting structure (for 500ns simulation of an octamer using gromacs-4.6 with martini22 force field). I could see some sharp jumps in rmsd (from 1.0A to 5.5A) at various time points in the trajectory.I would like to know whether anybody has faced this kind of problem and also how to go about with it?
Thank you,
with regards,
Anu
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- anuvc84
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Topic Author
- Visitor
11 years 1 month ago #1468
by anuvc84
Replied by anuvc84 on topic Error during nvt equilibration
Thank you..I used trjconv with -pbc nojump and generated a new .xtc file. Rmsd plot calculated from the new xtc file didnt show any jumps.
with regards
Anu
with regards
Anu
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