[gmx-users] Inconsistent shifts - is it something wrong with pbc

[ming ma]

Hi Justin,

Really appreciate your help. I have solved the problem following your
suggestion :)
I love this community~

2012/3/7 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> ming ma wrote:
>
>> Hi,
>>
>> Thanks for looking at this email. Before I asked this question, I have
>> read most of the related topics in gromacs's mailing list, but still can't
>> solve it.
>> When I was trying to do energy minimization of graphene with pbc, I got
>> several messages "there are # inconsistent shifts, check your topolgy."
>>  After the mimization is finished, the energy in extremely large (1.86e+05
>> kJ/mol), which is obviously wrong. To make sure that I haven't done any
>> stupid mistake, I have carried out energy minimization of the same system
>> using LAMMPS, and the results is reasonable (the energy is -205.14 eV). The
>> configuration of the system has also been checked by visualizing it in VMD,
>> and the PBC seems right.
>>
>> Below is my mdp file,
>>
>> ; energy minimization
>> integrator               = l-bfgs
>> nsteps                   = 5000
>> constraints              = none
>> emtol                    = 1.0
>> nstcgsteep               = 10 ; do a steep every 10 steps of cg
>> emstep                   = 0.01 ; used with steep
>> nbfgscorr                = 10
>> nstcomm                  = 0 ; frequecy of remove of com movement
>> Tcoupl                   = no
>> Pcoupl                   = no
>>
>> ; potential and neigbor related
>> coulombtype              = Cut-off
>> rcoulomb                 = 1.2
>> vdw-type                 = Switch
>> rvdw-switch              = 0.8
>> rvdw                     = 1.0
>> ; neighbor list related
>> rlist                    = 1.2
>> nstlist                  = 10
>> ns_type                  = grid
>>
>> pbc                      = xyz
>> ;output section
>> nstxout                  = 0
>> nstvout                  = 0
>> nstfout                  = 0
>> nstlog                   = 100
>> nstenergy                = 100
>> nstxtcout                = 0
>> xtc_precision            = 1000
>> xtc-grps                 =
>> energygrps               =
>>
>> And these are parts of the message I got during simulation,
>>
>> There were 262 inconsistent shifts. Check your topology
>> Will stop reporting inconsistent shifts
>>
>> This is the results I got
>> Low-Memory BFGS Minimizer converged to Fmax < 1 in 432 steps
>> Potential Energy  =  1.85767014488657e+05
>>
>> I also tried using the cg method instead of l-bfgs, after read the log
>> files carefully, I found these messages,
>>
>> Initializing Domain Decomposition on 4 nodes
>> Dynamic load balancing: no
>> Will sort the charge groups at every domain (re)decomposition
>> Initial maximum inter charge-group distances:
>>    two-body bonded interactions: 14.880 nm, Morse, atoms 8401 8540
>>  multi-body bonded interactions: 20.914 nm, G96Angle, atoms 8470 8540
>> Minimum cell size due to bonded interactions: 23.006 nm
>>
>> I checked the distances between the atoms it showed, obviously, this
>> large distance is caused by not having taken the pbc xyz into consideration
>> since the size of the simulation box is 15*15**6 nm. So does it mean I
>> haven't handle the pbc correctly? Since I notice in the message posted
>> before some of the 'inconsistent shifts' are also caused by pbc problems.
>>
>>
> Exactly, the periodicity is not being handled correctly.  Presumably
> you're dealing with an infinite sheet (thus bonds extend across periodic
> boundaries), and thus you need to set "periodic_molecules = yes" in the
> .mdp file.
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>



-- 
Dr. Ming MA
Department of  Chemistry, University College London
London Centre for Nanotechnology
17-19 Gordon Street
London
WC1H 0AH
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120307/bc64a9d0/attachment.html>