[gmx-users] Eror: No parallel Ewald use PME instead!

[Mark Abraham]

Thanks for providing a small fraction of the information for which Justin
asked. You stand a much better chance of ever getting an answer from
volunteers if you provide more detail than you think could ever be
relevant. :-)

Mark


On Wed, Jun 4, 2014 at 7:39 PM, Ali Alizadeh <ali.alizadehmojarad at gmail.com>
wrote:

> Dear Justin,
>
> here is my mdp file:
>
> title = Liquid CO2 NVT
> ; Run parameters
> integrator = md-vv
> nsteps = 2000000
> dt = 0.001
> emtol = 1.0
> emstep          = 0.0001
> ; Output control
> nstxout = 1000
> nstvout = 1000
> nstenergy = 1000
> nstlog = 100
> ; Bond parameters
> continuation = no
> constraint_algorithm = lincs
> constraints = all-bonds
>
> ; Neighborsearching
> ns_type = grid
> nstlist = 5
> rlist = 1.25
> rcoulomb = 1.25
> rvdw = 1.25
> ; Electrostatics
> coulombtype = ewald
> fourierspacing = 0.6
> ; Temperature coupling is on
> tcoupl = nose-hoover
> tc-grps = system
> tau_t = 0.1
> ref_t = 300
> ; Pressure coupling is off
> pcoupl = no
> ; Periodic boundary conditions
> pbc = xyz ; 3-D PBC
> ; Dispersion correction
> DispCorr = EnerPres
> ; Velocity generation
> gen_vel = yes
> gen_temp = 300
> gen_seed = -1
>
>
>
>
> On 6/4/14, 8:29 AM, Ali Alizadeh wrote:
> > Dear Mark,
> >
> > In my first simulation we had these lines:
> >
> > ; Electrostatics
> > coulombtype    = PME        ; Particle Mesh Ewald for long-range
> > electrostatics
> > pme_order    = 4        ; cubic interpolation
> > fourierspacing    = 0.12        ; grid spacing for FFT
> >
> > -----------------------
> >
> > ; Electrostatics
> > coulombtype    = ewald        ; Particle Mesh Ewald for long-range
> > electrostatics
> > fourierspacing    = 0.6        ; grid spacing for FFT
> >
> > -----------------
> >
> > My system in 2nd case is equilibrated.
> >
>
> For anyone to make sense of what you're doing, you'll need to provide
> complete
> .mdp files (those settings are not the only determining factors of the
> validity
> of the model physics) and evidence of what you're deciding is equilibrated,
> stable, etc (i.e. real numbers and output from whatever relevant analysis).
>
> -Justin
>
> > On Wed, Jun 4, 2014 at 4:35 PM, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> >>
> >>
> >>
> >> On Wed, Jun 4, 2014 at 12:42 PM, Ali Alizadeh <
> >> ali.alizadehmojarad at gmail.com> wrote:
> >>
> >>> Dear Mark,
> >>>
> >>> Thank you for your reply.
> >>>
> >>> When you do not change any parameters except one thing in mdp file(PME
> to
> >>>
> >>> ewald as the paper said that)and then your system converges, for me it
> means the problem is related to
> >>>
> >>> choosing the right method for  calculation of the electrostatic
> potential energy. What's your point on it?
> >>>
> >>>
> >> My point is that a flawed model physics, or a flawed system preparation,
> >> can get lucky and run stably, or not. On the information given, there is
> no
> >> reason to suppose that changing the kind of reciprocal-space
> approximation
> >> is relevant. Last time I heard a report like this, the person had
> changed
> >> various nonbonded settings "to make things run faster," and in so doing
> >> produced a junk model physics.
> >>
> >> Mark
> >>
> >>
> >>> -----
> >>>
> >>> Mark wrote:
> >>>
> >>> Hi,
> >>>
> >>> What makes you think the PME algorithm, rather than your choices of
> >>> settings for it (and twenty other things), is the problem?
> >>>
> >>> Mark
> >>>
> >>>
> >>> On Wed, Jun 4, 2014 at 7:57 AM, Ali Alizadeh <ali.alizadehmojarad at
> gmail.com <
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>>
> >>> wrote:
> >>>
> >>>> * Dear All users,
> >>> *
> >>>>> * I have encounter this error:
> >>> *>>* -------------
> >>> *>* Fatal error:
> >>> *>* No parallel Ewald. Use PME instead.
> >>> *>* --------------
> >>> *>>* I used 8 cores and gromacs 4.5.5, for doing my calculations. I
> should use
> >>> *>* ewald method because
> >>> *>>* my system can not converge using PME it heats up my system. Are
> there any
> >>> *>* suggestions?
> >>> *>>>>* --
> >>> *>* Sincerely
> >>> *>>* Ali Alizadeh
> >>> *>* --*
> >>>
>
> --
> Sincerely
>
> Ali Alizadeh
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * 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.
>