Parul tew wrote:
Dear GMX users,
I am facing problem while doing energy minimization before the
molecular dynamic simulation step of a system consisting of protein,
membrane, water and 14 ions.
The minim.mdp file is as follows
-------------------------------------------------------------------------------------------------------------
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest
descent minimization)
emtol = 1000.0 ; Stop minimization when the
maximum force < 1000.0 kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of
(minimization) steps to perform
; Parameters describing how to find the neighbors of each atom and how
to calculate the interactions
nstlist = 1 ; Frequency to update the
neighbor list and long range forces
ns_type = grid ; Method to determine neighbor
list (simple, grid)
rlist = 1.2 ; Cut-off for making
neighbor list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic
interactions
rcoulomb = 1.2 ; Short-range electrostatic cut-off
rvdw = 1.2 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions
*---------------------------------------------------------------------------------------------------------*
when I run this using the command
* *
*grompp –f minim.mdp –c system_sol_ions.gro -p topol.top –o em.tpr *
then I invoked mdrun which gave following error
--------------------------------------------------------------------------------------------------------
Reading file topol.tpr, VERSION 4.0.7 (single precision)
Loaded with Money
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
Step= 14, Dmax= 1.2e-06 nm, Epot= 3.03531e+22 Fmax= inf,
atom= 1417
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 3.0353124e+22
Maximum force = inf on atom 1417
Norm of force = inf
-----------------------------------------------------------------
After this I changed the
emstep = 0.1 ; Energy step size
nsteps = 5000 ; Maximum number of (minimization) steps to perform
constraints = none
After these changes the no of steps increased to 18 but still the system
did not converge and potential energy is very high
----------------------------------------------------------------------------------------------------------
Reading file em.tpr, VERSION 4.0.7 (single precision)
Loaded with Money
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 5000
Step= 17, Dmax= 1.5e-06 nm, Epot= 3.03531e+22 Fmax= inf,
atom= 1417
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 18 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 3.0353124e+22
Maximum force = inf on atom 1417
Norm of force = inf
----------------------------------------------------------------------------------------------------------------
What changes can I do in my minim.mdp file to converge my system and get
a negative value of Epot.
No amount of changes to the .mdp file will solve this. If you have infinite
forces, that indicates atomic overlap between some elements of the system that
cannot be resolved. The environment around atom 1417 is problematic. Look at
it in a visualization program and diagnose why it's happening. Then generate a
more stable configuration and try again.
-Justin
The topol.top file looks
--------------------------------------------------------------------------------------------------
[ system ]
; Name
protein
128-Lipid DPPC Bilayer
[ molecules ]
; Compound #mols
Protein_A 1
DPPC 121
SOL 11107
CL- 14
-----------------------------------------------------------------------------------------------------
Thanks,
Parul
--
========================================
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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