[gmx-users] MPI error in gromacs 4.6
Justin Lemkul
jalemkul at vt.edu
Mon Mar 24 13:05:29 CET 2014
On 3/24/14, 7:56 AM, Pavan Kumar wrote:
> It might be some typographical errors.
> Check the mdp file thoroughly. I think semicolon is required for the last
> line in your mdp file
>
Semicolons are never required; they're comments and are ignored by grompp.
-Justin
>
> On Mon, Mar 24, 2014 at 5:18 PM, Ankita Naithani
> <ankitanaithani at gmail.com>wrote:
>
>> Hi Pavan,
>> Thank you for your response. I am trying to generate the tpr file with the
>> following parameter;
>> ; Neighborsearching
>> ns_type = grid ; search neighboring grid cells
>> nstlist = 5 ; 25 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)
>> rlistlong = 1.0 ; long-range neighborlist cutoff (in nm)
>> cutoff-scheme = Verlet
>>
>> But, I get a warning of Unknown left-hand 'cutoff-scheme' in parameter
>> file.
>>
>>
>> On Mon, Mar 24, 2014 at 11:26 AM, Pavan Kumar <kumar.pavan006 at gmail.com
>>> wrote:
>>
>>> Hello Ankita
>>> You have to just include the following line in your mdp file
>>> cutoff-scheme=Verlet
>>> And run your grompp with the modfied mdp file to generate tpr file and
>> then
>>> mdrun.
>>> Hope this doesn't give you the same error
>>>
>>>
>>> On Mon, Mar 24, 2014 at 4:47 PM, Ankita Naithani
>>> <ankitanaithani at gmail.com>wrote:
>>>
>>>> Hi,
>>>>
>>>> I am trying to run a simulation of my protein (monomer ~500 residues).
>> I
>>>> had few questions and erors regarding the same.
>>>> I have previously run the simulation of the apo form of the same
>> protein
>>>> using Gromacs 4.5.5 which was available at the cluster facility I was
>>> using
>>>> and also which is installed in my system. However, when I tried to run
>>> the
>>>> holo form, I got error :
>>>> Fatal error:
>>>> 11 particles communicated to PME node 106 are more than 2/3 times the
>>>> cut-off out of the domain decomposition cell of their charge group in
>>>> dimension y.
>>>> This usually means that your system is not well equilibrated.
>>>> For more information and tips for troubleshooting, please check the
>>> GROMACS
>>>> website at http://www.gromacs.org/Documentation/Errors
>>>>
>>>> This I figured out could be solved using a lower timestep as my
>> previous
>>>> timestep was 4fs and now I have reduced it to 3fs which should work
>> fine
>>>> now.
>>>> However, after producing the tpr file for production run in my GROMACS
>>>> 4.5.5, I realised that the grant for the cluster facility is over and
>> the
>>>> new clusters which I am trying to set up the same protein for support
>>> only
>>>> gromacs 4.6. I am trying to run the code in these clusters and I get he
>>>> following error:
>>>>
>>>>
>>>> -------------------------------------------------------
>>>> Program mdrun_mpi, VERSION 4.6.3
>>>> Source code file: /home/gromacs-4.6.3/src/kernel/runner
>>>> .c, line: 824
>>>>
>>>> Fatal error:
>>>> OpenMP threads have been requested with cut-off scheme Group, but these
>>> are
>>>> only
>>>> supported with cut-off scheme Verlet
>>>> For more information and tips for troubleshooting, please check the
>>> GROMACS
>>>> website at http://www.gromacs.org/Documentation/Errors
>>>>
>>>>
>>>
>> ---------------------------------------------------------------------------------
>>>>
>>>> 1. I wanted help with my mdp options to make it compatible.
>>>> 2. Since my pevious calculations were based on gromacs 4.5.5, switching
>>> to
>>>> gromacs 4.6, would that break the continuity of the run or would that
>>> bring
>>>> about differences in the way the trajectories would be analysed?
>>>>
>>>>
>>>> Below, is my mdp file
>>>> title = production MD
>>>> ; Run parameters
>>>> integrator = md ; leap-frog algorithm
>>>> nsteps = 33333333 ; 0.003 * 33333333 = 100000 ps or 100 n
>>>> dt = 0.003 ; 3 fs
>>>> ; Output control
>>>> nstxout = 0 ; save coordinates every 2 ps
>>>> nstvout = 0 ; save velocities every 2 ps
>>>> nstxtcout = 1000 ; xtc compressed trajectory output every 5
>> ps
>>>> nstenergy = 1000 ; save energies every 5 ps
>>>> nstlog = 1000 ; update log file every 5 ps
>>>> energygrps = Protein ATP
>>>> ; Bond parameters
>>>> constraint_algorithm = lincs ; holonomic constraints
>>>> constraints = all-bonds ; 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 = 5 ; 25 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)
>>>> rlistlong = 1.0 ; long-range neighborlist 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
>>>> nstcomm = 10 ; remove com every 10 steps
>>>> ; Temperature coupling is on
>>>> tcoupl = V-rescale ; modified Berendsen thermostat
>>>> tc-grps = Protein Non-Protein ; two coupling groups - more
>>>> accurate
>>>> tau_t = 0.1 0.1 ; time constant, in ps
>>>> ref_t = 318 318 ; reference temperature, one for each
>>> group,
>>>> in K
>>>> ; Pressure coupling is off
>>>> pcoupl = berendsen ; Berendsen thermostat
>>>> pcoupltype = isotropic ; uniform scaling of box vectors
>>>> tau_p = 1.0 ; time constant, in ps
>>>> ref_p = 1.0 ; reference pressure, in bar
>>>> compressibility = 4.5e-5 ; isothermal compressibility of water,
>> bar^-1
>>>> ; Periodic boundary conditions
>>>> pbc = xyz ; 3-D PBC
>>>> ; Dispersion correction
>>>> DispCorr = EnerPres ; account for cut-off vdW scheme
>>>> ; Velocity generation
>>>> gen_vel = yes ; Velocity generation is on
>>>> gen_temp = 318 ; reference temperature, for protein in K
>>>>
>>>>
>>>>
>>>>
>>>> Kind regards--
>>>> Ankita Naithani
>>>> --
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>>>>
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>>>
>>>
>>>
>>> --
>>> Cheers
>>> Pavan
>>> --
>>> Gromacs Users mailing list
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>>
>>
>>
>> --
>> Ankita Naithani
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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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 601
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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