[gmx-users] -rerun with energygrps
nedomacho at gmail.com
Tue Apr 10 04:07:51 CEST 2018
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.
On 4/9/2018 7:12 PM, Mark Abraham wrote:
> What version is this? What does gmx compare report amwhen comparing the two
> tpr files?
> 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
>> 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,
>> Gromacs Users mailing list
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users