[gmx-users] problem regarding cut-off and the PME grid spacing
Justin Lemkul
jalemkul at vt.edu
Thu Apr 21 11:50:45 CEST 2016
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
>>>>>>>
>>>>>>> * 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.
>>>>>>>
>>>>>>> --
>>>>>> 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.
>>>>>>
>>>>>> --
>>>>> 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.
>>>>>
>>>>> --
>>>> 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.
>>>>
>>>>
>> --
>> ==================================================
>>
>> 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
>>
>> * 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.
>>
--
==================================================
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
==================================================
More information about the gromacs.org_gmx-users
mailing list