[gmx-users] Problem on pbc atom

[Justin Lemkul]

On 10/19/19 12:48 PM, Mahsa Rezaei wrote:
> Dear gromacs users,
> I am using following pull code in md simulation
> for pulling a ligand across the plasma membrane model.
> My size box is 8.52807   8.52807  14.00000.
> And the pull distance is less than one-half the length of the box vector
> along.pull distance is 6 nm.
>
>
> when I execute this command,I got warning:
>
> gmx grompp -f md_pull.mdp -c complex.gro -p topol.top -r complex.gro -n
> index.ndx -o pull.tpr
>
>
> WARNING 1 [file md_pull.mdp]:
>    Pull group 1 has atoms at a distance larger than 0.9 times half the box
>    size from the PBC atom (27119). If atoms are or will more beyond half the
>    box size from the PBC atom, the COM will be ill defined.
>
> Pull group  natoms  pbc atom  distance at start  reference at t=0
>         1     54231     27120
>         2         4         2      -3.769 nm         -3.769 nm
> Estimate for the relative computational load of the PME mesh part: 0.10
> This run will generate roughly 1238 Mb of data
>
> Fatal error:
> Too many warnings (1).
> If you are sure all warnings are harmless, use the -maxwarn option.
>
> What should I do?
> I would be very appreciated for your such kind helps.

The reference for determining periodic distances is simply the numerical 
middle of the atom selection, which may not have any resemblance to the 
geometric center. If your group(s) is(are) non-spherical in nature, you 
need to select an appropriate atom for grompp and mdrun to compute the 
periodic distances.

-Justin

> My mdp file  :
>
> integrator              = md
> dt                      = 0.002
> nsteps                  = 290000 ; 580 ps
> ; Output parameters
> nstlog                  = 1000
> nstxout                 = 500   ; every 1 ps
> nstvout                 = 500
> nstfout                 = 500
> nstxtcout               = 500    ; every 1 ps
> nstcalcenergy           = 500
> nstenergy               = 500
>
> cutoff-scheme           = Verlet
> nstlist                 = 20
> rlist                   = 1.2
> coulombtype             = pme
> rcoulomb                = 1.2
> vdwtype                 = Cut-off
> vdw-modifier            = Force-switch
> rvdw_switch             = 1.0
> rvdw                    = 1.2
> ;
> tcoupl                  = Nose-Hoover
> tc_grps                 = PROT  MEMB_LIG  SOL_ION
> tau_t                   = 1.0    1.0    1.0
> ref_t                   = 303.15 303.15 303.15
> ;
> pcoupl                  = Parrinello-Rahman
> pcoupltype              = semiisotropic
> tau_p                   = 5.0
> compressibility         = 4.5e-5  4.5e-5
> ref_p                   = 1.0     1.0
> ;
> constraints             = h-bonds
> constraint_algorithm    = LINCS
> continuation            = yes
> ;
> nstcomm                 = 100
> comm_mode               = linear
> comm_grps               = PROT MEMB_LIG SOL_ION
> ;
> refcoord_scaling        = com
>
> ; Pull code
> pull                       = yes
> pull_ncoords               = 1         ; only one reaction coordinate
> pull_ngroups               = 2
> pull_group1_name           = BILAYER
> pull_group2_name           = LIG
> pull_coord1_type           = umbrella  ; harmonic potential
> pull_coord1_geometry       = direction
> pull_coord1_vec            = 0.0 0.0 1.0
> pull_coord1_groups         = 1 2
> pull_coord1_start          = yes       ; define initial COM distance > 0
> pull_coord1_rate           = 0.01      ; 0.01 nm per ps =10nm per ns
> pull_coord1_k              = 2000      ; kJ mol^-1 nm^-2
> pull_nstxout               = 500        ; every 1 ps
> pull_nstfout               = 500        ; every 1 ps
>
>
>
>
>
> [image: Mailtrack]
> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&>
> Sender
> notified by
> Mailtrack
> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&>
> 10/19/19,
> 08:14:02 PM

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================