[gmx-users] Charged group problem

[Justin Lemkul]

On 8/12/15 9:30 AM, Adriana Garro wrote:
> Dear users,
>
> My system contains peptide + TFE + water in an octahedron box.
> I am using oplsaa.ff
> I am trying to do EM but running this command
>
> grompp -f em.mdp -c  C22_TFE-W.gro -p topol.top -o em.tpr
>
> the next error message come up
>
> WARNING 1 [file em.mdp]:
>    The sum of the two largest charge group radii (2.045171) is larger than
>    rlist (1.000000)
>
> I am afraid of changing the em.mdp parameters because as I understand these
> are the correct for my force field.
> I'd really appreciate suggestions!

Assign smaller charge groups (fewer atoms), or use the Verlet cutoff scheme, for 
which charge groups are irrelevant (it's more accurate than the old group 
scheme, anyway).

-Justin

> Thanks in advance
>
>
> Adriana
>
>
> here a part of the em.mdp file
>
> nstlist        = 1
> ns_type        = grid
> rlist          = 1.0
> coulombtype    = PME                        ; Use particle-mesh ewald
> rcoulomb       = 1.0
> rvdw           = 1.0
>
> I read that large charge groups indicate that a fair number of atoms have
> been included in the same charge group. Usually only two or three atoms are
> in a charge group, rendering them fairly small.
>
> Looking in the TFE.itp, it's true, the whole molecule is in the same
> charged group
>
>       1   opls_160      1    TFE   CA3F      1      0.126     12.011   ;
> qtot 0.126
>       2   opls_161      1    TFE   CF3F      1      0.532     12.011   ;
> qtot 0.658
>       3   opls_162      1    TFE   OH3F      1     -0.635    15.9994   ;
> qtot 0.023
>       4   opls_163      1    TFE   HO3F      1      0.429      1.008   ;
> qtot 0.452
>       5   opls_164      1    TFE   F13F      1     -0.206    18.9984   ;
> qtot 0.246
>       6   opls_164      1    TFE   F23F      1     -0.206    18.9984   ;
> qtot 0.04
>       7   opls_164      1    TFE   F33F      1     -0.206    18.9984   ;
> qtot -0.166
>       8   opls_165      1    TFE   H13F      1      0.083      1.008   ;
> qtot -0.083
>       9   opls_165      1    TFE   H23F      1      0.083      1.008   ;
> qtot 0
> ***********************************************************
> Dra. Adriana D. Garro
> Química Medicinal
> Facultad de Química, Bioquímica y Farmacia
> Universidad Nacional de San Luis
> IMASL-CONICET
> San Luis, Argentina
>
> Tel..............:+54 266 4424689  int 6153
> e-mail...: adgarro at unsl.edu.ar
> e-mail...:  adrianagarrosl at gmail.com
>
>
> **********************************************************
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================