On 9/16/13 3:06 AM, shahab shariati wrote:
Dear Justin
Very thanks for your reply.
You said "I suspect your Gromacs version is somewhat outdated, as recent
versions account for periodicity when
making this check". I used 4.5.5 version of gromacs. What version of
gromacs is more appropriate for my case.
When in doubt, always upgrade to the newest version, which is currently 4.6.3.
I can't remember when the issue was fixed.
Based on your suggestion, I used -maxwarn option for grompp. Then I used
-nt 1 option for mdrun,
but this step takes too long and
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
Warning: 1-4 interaction between 434 and 407 at distance 3.023 which is
larger than the 1-4 table size 2.200 nm
These are ignored for the rest of the simulation
******************** This usually means your system is exploding,
********************
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
step 23: Water molecule starting at atom 10613 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
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 2122 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 1.4310875e+05
Maximum force = 2.7179752e+04 on atom 5271
Norm of force = 4.0253470e+02
In this case, it is pretty clear that there is actually something wrong with the
input coordinates.
--------------------------------------------------------------------------------------
my em.mdp file is as follows:
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
--------------------------------------------------------------------------------------
gro, edr, trr and lof file were created.
I increased emstep from 0.01 to 0.1 and I used constraints = none in mdp
file, but result are the same.
Increasing emstep does not make sense. If anything, you should be decreasing it
to try to take smaller steps and resolve clashes. In any case, the output tells
you where the maximum force is. Fire up your favorite visualization software,
look at that atom and the things around it, and figure out what is going on.
Is this minimization completely true?
Can I use created gro file of this minimization for next step
(equilibration)?
No, the forces are far too high to be useful. Anything you do will simply
crash.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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