[gmx-users] Re: grompp for minimization: note & warning
shahab shariati
shahab.shariati at gmail.com
Wed Sep 18 09:38:57 CEST 2013
Dear Tsjerk
Thanks for your consideration.
My system contains 2 components: (DOPC & cholesterol) lipids + water
molecules.
I get force field parameters from lipid book (for dopc and cholesterol).
I used input coordinate file (system.gro) from following web site:
http://people.su.se/~jjm/Stockholm_Lipids/Downloads.html
em.mdp file is as follows:
-------------------------------------------------------------------------------------
; em.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
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
-----------------------------------------------------------------------------------------
For doing minimization, I used following command:
grompp -f em.mdp -c system.gro -p topol.top -o em.tpr
and then I get following result:
-------------------------------------------------------------------------------------
WARNING 1 [file topol.top, line 32]:
3632 non-matching atom names
atom names from topol.top will be used
atom names from system.gro will be ignored
Analysing residue names:
Warning: file does not end with a newline, last line:
IB+ Ion
There are: 128 Other residues
There are: 1706 Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Number of degrees of freedom in T-Coupling group rest is 29019.00
Largest charge group radii for Van der Waals: 1.541, 1.514 nm
Largest charge group radii for Coulomb: 0.079, 0.079 nm
WARNING 2 [file em.mdp]:
The sum of the two largest charge group radii (3.054313) is larger than
rlist (1.200000)
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 72x72x72, spacing 0.111 0.120 0.116
Estimate for the relative computational load of the PME mesh part: 0.62
NOTE 1 [file em.mdp]:
The optimal PME mesh load for parallel simulations is below 0.5
and for highly parallel simulations between 0.25 and 0.33,
for higher performance, increase the cut-off and the PME grid spacing
This run will generate roughly 133 Mb of data
There was 1 note
There were 2 warnings
-------------------------------------------------------------------------------------
I used -maxwarn option and I obtained em.tpr file.
Then, for doing minimization, I used following command:
mdrun -s em.tpr -o em.trr -c em.gro -e em.edr -g em.log
and then I get following result:
-------------------------------------------------------------------------------------
Reading file em.tpr, VERSION 4.5.1 (single precision)
Starting 4 threads
Making 2D domain decomposition 1 x 2 x 2
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
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 881 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 2.1828770e+05
Maximum force = 1.3656898e+04 on atom 618
Norm of force = 5.1748779e+02
-------------------------------------------------------------------------------------
When I see created gro file (em.gro) by VMD, some dopc or cholesterol
molecules are broken to 2 or 3 parts.
I tested different ways:
1) change of parameters in em.mdp file ( emstep, nstep, EM algorithm )
2) change of box size
3) I used the newest version of gromacs (4.6.3)
But, unfortunatele, my problem was not solved.
Certainly, I can not use this structure for next step (equilibration).
How to solve this problem.
Any help will highly appreciated.
Best wishes for you
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