On 9/15/13 3:44 AM, shahab shariati wrote:
Dear gromacs users
My system contains 3 components: DOPC & cholesterol lipids + drug + water
molecules.
In minimization step, when I use
grompp -f em.mdp -c system.gro -p topol.top -o em.tpr,
I encountered with following note and warning:
WARNING 1 [file em.mdp]:
The sum of the two largest charge group radii (6.940482) is larger than
rlist (1.200000)
http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb
You probably have molecules split across PBC in the input coordinate file.
There's nothing wrong in that case.
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
-----------------------------------------------------------------------------------
For energy minimization, this doesn't really matter.
My 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
-------------------------------------------------------------------------------------
I dont like to use -maxwarn option. How to modify parameters in em.mdp file
to resolve note an warning.
If you do, in fact, have broken molecules in the input coordinates, then
-maxwarn is actually OK. I suspect your Gromacs version is somewhat outdated,
as recent versions account for periodicity when making this check.
-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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