[gmx-users] Charged group problem

[Adriana Garro]

Thank you Justin, as friendly as ever!

Adriana

***********************************************************
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


**********************************************************

2015-08-12 17:27 GMT-03:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> 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
>
> ==================================================
> --
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