- Posts: 1
Energy minimization fails using PW with PME
- MelanieK
-
Topic Author
- Offline
- Fresh Boarder
Less
More
7 years 6 months ago #5934
by MelanieK
Energy minimization fails using PW with PME was created by MelanieK
Dear all,
I try to simulate a deprotonated polyacrylic acid chain (20-mer) with water (7858 PW molecules) and sodium counter ions in a cubic box with 10 nm edge length. I'm using GROMACS 5.1.2. As long-range electrostatic interactions are important for me I would like to use the polarizable water model with PME. However, the energy minimization fails with the following error:
Step= 416, Dmax= 1.5e-02 nm, Epot= -3.44418e+05 Fmax= 7.72787e+03, atom= 4063
Step= 417, Dmax= 1.7e-02 nm, Epot= -3.58572e+05 Fmax= 1.80823e+07, atom= 3698
Step= 426, Dmax= 8.2e-05 nm, Epot= -3.62271e+05 Fmax= 2.84181e+07, atom= 3698
Step= 430, Dmax= 1.2e-05 nm, Epot= -3.62988e+05 Fmax= 3.06918e+07, atom= 3698
Step= 434, Dmax= 1.8e-06 nm, Epot= -3.63101e+05 Fmax= 3.10578e+07, atom= 3698
Step= 436, Dmax= 1.1e-06 nm, Epot= -nan Fmax= 1.16874e+03, atom= 4062
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 10 (which may not be possible for your system). It
stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.
I used this mdp file based on new-rf.mdp ( www.cgmartini.nl/images/parameters/examp...tini_v2.x_new-rf.mdp ):
; minim.mdp - used as input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent minimization)
; start time and timestep in ps =
tinit = 0.0
dt = 0.01
nsteps = 50000
; NEIGHBOURLIST and MARTINI
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005
coulombtype = PME
rcoulomb = 1.1
epsilon_r = 2.5
epsilon_rf = 0
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1
; MARTINI and CONSTRAINTS
constraints = none
constraint_algorithm = Lincs
I also tried smaller time steps but the error was the same. Interestingly, when I use reaction-field as suggested in the standard mdp file, I don't get this error. The minimization runs without any problem.
What does this mean? What do I have to change in my mdp file in order to use PME correctly?
Thank you for your help!
Melanie
I try to simulate a deprotonated polyacrylic acid chain (20-mer) with water (7858 PW molecules) and sodium counter ions in a cubic box with 10 nm edge length. I'm using GROMACS 5.1.2. As long-range electrostatic interactions are important for me I would like to use the polarizable water model with PME. However, the energy minimization fails with the following error:
Step= 416, Dmax= 1.5e-02 nm, Epot= -3.44418e+05 Fmax= 7.72787e+03, atom= 4063
Step= 417, Dmax= 1.7e-02 nm, Epot= -3.58572e+05 Fmax= 1.80823e+07, atom= 3698
Step= 426, Dmax= 8.2e-05 nm, Epot= -3.62271e+05 Fmax= 2.84181e+07, atom= 3698
Step= 430, Dmax= 1.2e-05 nm, Epot= -3.62988e+05 Fmax= 3.06918e+07, atom= 3698
Step= 434, Dmax= 1.8e-06 nm, Epot= -3.63101e+05 Fmax= 3.10578e+07, atom= 3698
Step= 436, Dmax= 1.1e-06 nm, Epot= -nan Fmax= 1.16874e+03, atom= 4062
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 10 (which may not be possible for your system). It
stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.
I used this mdp file based on new-rf.mdp ( www.cgmartini.nl/images/parameters/examp...tini_v2.x_new-rf.mdp ):
; minim.mdp - used as input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent minimization)
; start time and timestep in ps =
tinit = 0.0
dt = 0.01
nsteps = 50000
; NEIGHBOURLIST and MARTINI
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005
coulombtype = PME
rcoulomb = 1.1
epsilon_r = 2.5
epsilon_rf = 0
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1
; MARTINI and CONSTRAINTS
constraints = none
constraint_algorithm = Lincs
I also tried smaller time steps but the error was the same. Interestingly, when I use reaction-field as suggested in the standard mdp file, I don't get this error. The minimization runs without any problem.
What does this mean? What do I have to change in my mdp file in order to use PME correctly?
Thank you for your help!
Melanie
Please Log in or Create an account to join the conversation.
- bart
-
- Away
- Admin
Less
More
- Posts: 98
7 years 6 months ago #5966
by bart
Replied by bart on topic Energy minimization fails using PW with PME
Hi Melanie,
The minimisation can get stuck at a local minimum where it can not escape from. Therefore it is not capable of finding a state which has no particles affected by the aimed force or lower. However, MARTINI is more stable than AA force fields and often has no problem with proceding with the equilibration, even if the EM did not converge to the stated max force. I think yours is still acceptable and continuing should not cause problems.
Cheers and please let me know if the problem persists.
Bart
PhD student at the MARTINI lab
The minimisation can get stuck at a local minimum where it can not escape from. Therefore it is not capable of finding a state which has no particles affected by the aimed force or lower. However, MARTINI is more stable than AA force fields and often has no problem with proceding with the equilibration, even if the EM did not converge to the stated max force. I think yours is still acceptable and continuing should not cause problems.
Cheers and please let me know if the problem persists.
Bart
PhD student at the MARTINI lab
Please Log in or Create an account to join the conversation.
- Pim
-
- Offline
- Expert Boarder
Less
More
- Posts: 105
7 years 5 months ago #6003
by Pim
Replied by Pim on topic Energy minimization fails using PW with PME
I indeed also experience this from time to time when using the polarisable force field and dissolved polypeptides. As Bart says, usually it is not really a big problem. Although starting from the end point with forces on the order of 1e7 might be unstable (not per se), you can either resolvate using a different random seed (-seed flag in gmx solvate) and try again, or take the structure from a step where the forces were not as high (e.g. step 416 in your example, 1e3 or 1e4 is usually fine).
Please Log in or Create an account to join the conversation.
Time to create page: 0.205 seconds