[gmx-users] Lost particles while sorting
Alex
nedomacho at gmail.com
Thu Nov 2 01:26:40 CET 2017
Mark,
Could you please share your email address, so I can send you the tpr
privately? I don't want this work to be public just yet, if that's okay.
Thanks,
Alex
On 11/1/2017 4:42 PM, Mark Abraham wrote:
> Hi,
>
> We have had several reports of "lost particles while sorting" but we would
> like a .tpr on an issue on redmine.gromacs.org to be able to investigate,
> please!
>
> Mark
>
> On Wed, Nov 1, 2017 at 10:19 PM Alex <nedomacho at gmail.com> wrote:
>
>> Hi all,
>>
>> I am using walls in the cowboy mode, GMX v. 2016.3, system is a porous
>> membrane (periodic in XY) with water and ions -- everything works fine with
>> pbc=xyz and no walls. With walls, mdrun throws "Software inconsistency
>> error: Lost particles while sorting."
>>
>> mdp exerpt below:
>>
>> pbc = xy
>> nwall = 2
>> wall-type = 12-6
>> wall-r-linpot = 0.0
>> wall_atomtype = opls_996 opls_996
>> wall-ewald-zfac = 3
>> periodic_molecules = yes
>> ns_type = grid
>> rlist = 1.0
>> coulombtype = pme
>> ewald-geometry = 3dc
>> fourierspacing = 0.135
>> rcoulomb = 1.0
>> rvdw = 1.0
>> vdwtype = cut-off
>> cutoff-scheme = Verlet
>>
>> This uses a custom type "opls_996" properly defined in ffnonbonded of the
>> FF (custom OPLSAA). Any suggestions? I can provide more info, if needed.
>>
>> Thank you,
>>
>> Alex
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