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

[Ali Alizadeh]

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