[gmx-users] problem regarding cut-off and the PME grid spacing
Tuhin Samanta
samantatuhin1991 at gmail.com
Thu Apr 21 09:32:12 CEST 2016
The topology file for my system --------- HOD System like that ---
#include "oplsaa.ff/forcefield.itp"
; Include hod topology
#include "hod.itp"
[ system ]
;Name
HOD
[ molecules ]
; Compound #mols
HOD 102
.mdp file is like that -----
(FOR Energy minimization)
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent
minimization)
emtol = 0.1 ; Stop minimization when the maximum force
< 1000.0 kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 200000 ; Maximum number of (minimization) steps to
perform
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and
long range forces
ns_type = grid ; Method to determine neighbor list
(simple, grid)
rlist = 1.0 ; Cut-off for making neighbor list (short
range forces)
coulombtype = PME ; Treatment of long range electrostatic
interactions
rcoulomb = 1.0 ; Short-range electrostatic cut-off
rvdw = 1.0 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)
constraints = none
For Equilibritaion (NVT)
title = NVT equilibration of W10 RM
cpp = /lib/cpp
include = -I../top
integrator = md ; leap-frog integrator
nsteps = 500000 ; 2 * 10000 = 20 ns
dt = 0.002 ; 2 fs
; Output control
nstxout = 100 ; save coordinates every 0.1 ns
nstvout = 100 ; save velocities every 0.1 ns
nstenergy = 100 ; save energies every 0.1 ns
nstlog = 100 ; update log file every 0.1 ns
; Bond parameters
continuation = yes ; continuation from previous run
constraint_algorithm = lincs ; holonomic constraints
constraints = none ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 10 fs
rlist = 1.0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
optimize_fft = yes
; Temperature coupling is on
tcoupl = Berendsen ; modified Berendsen thermostat
tc-grps = System ; two coupling groups - more accurate
tau_t = 1.0 ; time constant, in ps
ref_t = 300 ; reference temperature, one for each group
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell
distribution
Please take a look . I am getting the error like that ------ 4 particles
communicated to PME node 4 are more than 2/3 times the cut-off out of the
domain decomposition cell of their charge group in dimension x. This
usually means that your system is not well equilibrated.
If you want I can send you my .itp file also.
Tuhin
On Wed, Apr 20, 2016 at 10:52 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 4/20/16 1:20 PM, Tuhin Samanta wrote:
>
>> I have done the energy minimization many times by taking previously
>> minimized structure.
>>
>>
> A box of water should be basically impossible to break. Either your .mdp
> or topology has problems. Since you've provided neither, there's not much
> anyone can do to help you. The diagnostic walkthrough that Mark linked is
> the best source of figuring it out. Short of that, provide us with your
> input topology and .mdp (copied and pasted if small enough for an email, or
> linked to a file-sharing service otherwise).
>
> -Justin
>
>
>
>>
>> On Wed, Apr 20, 2016 at 10:39 PM, Mark Abraham <mark.j.abraham at gmail.com>
>> wrote:
>>
>> Hi,
>>>
>>> On Wed, 20 Apr 2016 19:04 Tuhin Samanta <samantatuhin1991 at gmail.com>
>>> wrote:
>>>
>>> Thank Mark for your suggestion.
>>>>
>>>> I was trying to resolve the problem --------
>>>> " 4 particles communicated to PME node 4 are more than 2/3 times the
>>>> cut-off out of the domain decomposition cell of their charge group in
>>>> dimension x.
>>>> This usually means that your system is not well equilibrated."
>>>>
>>>> First of all I have done the energy minimization for long times for
>>>>
>>> proper
>>>
>>>> equilibriuation.
>>>>
>>>>
>>> Then what did you change? You may need to be more gentle.
>>>
>>> Secondly by changing rcut and PME mesh girding I have tried a lot. But
>>> it's
>>>
>>>> showing same error message.
>>>>
>>>>
>>> Those suggestions are made for perhaps improving performance, which is
>>> unrelated to your error. They just both happen to use the word PME...
>>>
>>> So can you please tell me any specific solution for this problem.
>>>
>>>>
>>>>
>>> They're all at
>>> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>>>
>>> Mark
>>>
>>> Thanking you,
>>>
>>>> Tuhin
>>>>
>>>>
>>>> On Wed, Apr 20, 2016 at 2:21 PM, Mark Abraham <mark.j.abraham at gmail.com
>>>> >
>>>> wrote:
>>>>
>>>> Hi,
>>>>>
>>>>> The information message and the actual error are separated in your log
>>>>>
>>>> file
>>>>
>>>>> with a bunch of punctuation because they're logically separate.
>>>>>
>>>>> Anyway, there should also have been a link to
>>>>> http://www.gromacs.org/Documentation/Errors which suggests some
>>>>>
>>>> strategies
>>>>
>>>>> for this issue.
>>>>>
>>>>> Mark
>>>>>
>>>>> On Wed, 20 Apr 2016 09:00 Tuhin Samanta <samantatuhin1991 at gmail.com>
>>>>> wrote:
>>>>>
>>>>> Hello ,
>>>>>>
>>>>>> My system involves water molecules in a box of 5x5x5 nm3. When I was
>>>>>>
>>>>> doing
>>>>>
>>>>>> the simulation for energy minimization I got n error message --
>>>>>>
>>>>>> The optimal PME mesh load for parallel simulations is below 0.5
>>>>>> and for highly parallel simulations between 0.25 and 0.33,
>>>>>> for higher performance, increase the cut-off and the PME grid
>>>>>>
>>>>> spacing
>>>
>>>>
>>>>>> 4 particles communicated to PME node 4 are more than 2/3 times the
>>>>>>
>>>>> cut-off
>>>>>
>>>>>> out of the domain decomposition cell of their charge group in
>>>>>>
>>>>> dimension
>>>
>>>> x.
>>>>>
>>>>>> This usually means that your system is not well equilibrated.
>>>>>>
>>>>>> I have changed the cut off and grid spacing but still it's showing
>>>>>>
>>>>> the
>>>
>>>> error message. I know it is the problem with the parallelization.
>>>>>>
>>>>> Also
>>>
>>>> I
>>>>
>>>>> have gone through the user forum's discussion. So can anyone please
>>>>>> suggest me how to get rid of that problem.
>>>>>>
>>>>>>
>>>>>> Thank you so much.
>>>>>> Best regards,
>>>>>> Tuhin
>>>>>> --
>>>>>> Gromacs Users mailing list
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>>>>> or
>>>
>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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