[gmx-users] -rerun with energygrps

[Alex]

This is 2018, I will compare later. The issue is mostly sort of solved, 
as I just moved all of electrostatics to 'cut-off' with a large radius 
for the rerun.

I first thought it was because the system was not neutral (ion + water 
without the counterion, so it refused to report the PME part), but same 
behavior with a counterion.

It would be interesting to see if you guys could independently reproduce 
this with me supplying just the mdp files. Just a 3x3x3 box with a 
single K+ ion and TIP4P water. em followed by 1 ns NPT (Berendsen) 
relax, followed by 10 ns NPT production test.

Alex


On 4/9/2018 7:12 PM, Mark Abraham wrote:
> Hi,
>
> What version is this? What does gmx compare report amwhen comparing the two
> tpr files?
>
> Mark
>
> On Mon, Apr 9, 2018, 22:54 Alex <nedomacho at gmail.com> wrote:
>
>> Hi all,
>>
>> Something funny is happening. I have a very simple system: an ion in bulk
>> TIP4P water running under OPLS-AA. mdp excerpt below:
>>
>> nstlist             =  20
>> pbc                 = xyz
>> periodic_molecules  = yes
>> ns_type             =  grid
>> rlist               =  1.0
>> coulombtype         =  pme
>> fourierspacing      =  0.135
>> rcoulomb            =  1.0
>> rvdw                =  1.0
>> vdwtype             =  cut-off
>> cutoff-scheme   = Verlet
>>
>> In order to determine ion-solvent interaction energy, i have a rerun mdp
>> that is identical to the one used for the actual simulation, but with
>>
>> energygrps = K SOL
>>
>> added. When applying gmx energy to the rerun edr, the only K-SOL options
>> are:
>>
>> 41  Coul-SR:K-SOL
>> 42  LJ-SR:K-SOL
>>
>> Nothing long-range. This has never been the case before and PME
>> contribution was always there.
>>
>> Any suggestions?
>>
>> Thank you,
>>
>> Alex
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