[gmx-users] MDRUN CRASH 2

[Luca Banetta]

Perfect. I made some modifications to the topology of the acetone molecule:
I connected the shell directley to the atom this way

[ polarization ]
;   atom      shell   functiontype  alpha nm^3
      1         11        1            0.001

and I made the exclusions inspired by topology in drude particle

[ exclusions]

1 2 3 4 5 6 7 8 9 10 11
2 3 4 5 6 7 8 9 10 11
3 4 5 6 7 8 9 10 11
4 1 2 3 5 6 7 8 9 10 11
5 6 7 8 9 10 11
6 7 8 9 10 11
7 8 9 10 11
8 9 10 11
9 10 11
10 11

As you suggested I tried to run the simulation with these parameters on one
core and, for now, it works!
Il 18/Giu/2016 11:38, "Justin Lemkul" <jalemkul at vt.edu> ha scritto:

>
>
> On 6/18/16 4:08 AM, Luca Banetta wrote:
>
>> Dear Justin,
>> Acording to our previous e-mails that are held because of eccessive
>> weight, is it possible in the end to produce a model with the use of a
>> shell particle for the acetone molecule?
>>
>>
> Yes, it is possible.
>
> -Justin
>
> --
> ==================================================
>
> 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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