[gmx-users] problem regarding cut-off and the PME grid spacing
Tuhin Samanta
samantatuhin1991 at gmail.com
Thu Apr 21 12:57:23 CEST 2016
please check it.......
[ moleculetype ]
; molname nrexcl
HOD 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_116 1 HOD OW 1 -0.8476
2 opls_117 1 HOD HW 1 0.4238
3 opls_805 1 HOD DW 1 0.4238
#ifndef FLEXIBLE
; [ settles ]
; OW funct doh dhh
; 1 0.101 0.16500
;[ exclusions ]
;1 2 3
;2 1 3
;3 1 2
#else
[ bonds ]
; i j funct length force.c.
1 2 1 0.1 345000 0.1 345000
1 3 1 0.102 266292 0.102 266292
[ angles ]
; i j k funct angle force.c.
2 1 3 1 105.7 583 105.7 583
Thanks,
Tuhin
On Thu, Apr 21, 2016 at 3:20 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 4/21/16 3:32 AM, Tuhin Samanta wrote:
>
>> 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.
>>
>>
> Yes, that's actually rather important; the .top itself just #includes the
> .itp and therefore contains no useful information.
>
> -Justin
>
>
> 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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>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>>>> posting!
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>>>>>>>>
>>>>>>>> or
>>>>>>>
>>>>>>
>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>
>>>>>>>
>>>>>>>> --
>>>>>>>>
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>>>>>>>
>>>>>> Gromacs Users mailing list
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>>>>>> --
>>>>>>
>>>>> Gromacs Users mailing list
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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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>>>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
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