Re: [gmx-users] Problem on pbc atom

2019-10-21 Thread 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  14.0.
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  = 29 ; 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   = 1.01.01.0
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





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--
==

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

jalem...@vt.edu | (540) 231-3129
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[gmx-users] Problem on pbc atom

2019-10-19 Thread Mahsa Rezaei 
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  14.0.
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.

My mdp file  :

integrator  = md
dt  = 0.002
nsteps  = 29 ; 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   = 1.01.01.0
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





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