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

[Justin Lemkul]

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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