[gmx-users] Re: grompp for minimization: note & warning

[shahab shariati]

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