Pulling not run

User discussions
,
1

GROMACS version: 2023.3
GROMACS modification: No

Hi,

I am trying to perform a pull with NP (fullerene) to membrane (POPC). But, I am when running a grompp I have no problems. At the moment of launching the pulling-md with gmx mdrun -deffnm this one freezes (the calculation does not die).
(1)


  gmx grompp -f pull.mdp -c 0_boxcomplete.gro -r 0_boxcomplete.gro -p ../topol.top -n index.ndx -maxwarn 4 -o ge_pull.tpr

I

gnoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Ignoring obsolete mdp entry 'optimize_fft'
Ignoring obsolete mdp entry 'ns_type'
Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
Setting the LD random seed to -1395788807

Generated 44 of the 990 non-bonded parameter combinations

Excluding 1 bonded neighbours molecule type 'F576'

Excluding 1 bonded neighbours molecule type 'POPS'

Excluding 1 bonded neighbours molecule type 'POPC'

Excluding 1 bonded neighbours molecule type 'NA+'

Excluding 1 bonded neighbours molecule type 'CL-'

Excluding 1 bonded neighbours molecule type 'W'
Pull group 1 'NP' has 2376 atoms
Pull group 2 'POPC' has 21984 atoms
Number of degrees of freedom in T-Coupling group System is 340536.00

Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K

Calculated rlist for 1x1 atom pair-list as 1.460 nm, buffer size 0.060 nm

Set rlist, assuming 4x4 atom pair-list, to 1.409 nm, buffer size 0.009 nm

Note that mdrun will redetermine rlist based on the actual pair-list setup

NOTE 1 [file pull.mdp]:
  You are using a plain Coulomb cut-off, which might produce artifacts.
  You might want to consider using PME electrostatics.


Pull group  natoms  pbc atom  distance at start  reference at t=0
       1      2376         1
       2     21984     21984       7.756 nm         15.512 nm

NOTE 2 [file pull.mdp]:
  This run will generate roughly 3293 Mb of data

(2)
gmx grompp -f pull.mdp -c 0_boxcomplete.gro -r 0_boxcomplete.gro -p ../topol.top -n index.ndx -maxwarn 4 -o ge_pull.tpr

(3) ; GENERAL INPUT FLAGS
title                  = 2.5ns equilibration NVT
cpp                    = /usr/bin/cpp
define                 =

; RUN FLAGS
integrator             = md
dt                     = 0.020
nsteps                 = 250000
pbc                    = xyz

; NON-BONDED INTERACTIONS FLAGS
ns_type                = grid
nstlist                = 10
rlist                  = 1.4
coulombtype            = cutoff
rcoulomb               = 1.4
vdwtype                = Cut-off
rvdw                   = 1.4

optimize_fft           = yes
fourierspacing         = 0.2

; TEMPERATURE COUPLING FLAGS
tcoupl                 = V-rescale
tc-grps                = System
tau_t                  = 1.0
ref_t                  = 310

; INITIAL STEP VELOCITIES FLAGS
gen_vel                = no
gen_temp               = 310
gen_seed               = -1

; PRESSURE COUPLING FLAGS
Pcoupl                 = no

; CONSTRAINTS
; None (see manual)

; Pull code
pull                    = yes
pull_ncoords            = 1
pull_ngroups            = 2
pull_group1_name        = NP
pull_group2_name        = POPC
pull_coord1_type        = umbrella
pull_coord1_geometry    = distance
pull_coord1_dim         = N N Y
pull_coord1_groups      = 1 2
pull_coord1_start       = yes
pull_coord1_rate        = 0.05
pull_coord1_k           = 1500
pull_group1_pbcatom     = 1
pull_group2_pbcatom     = 21984
pull_pbc_ref_prev_step_com = yes
pull_coord1_init        = 7.756

; DISTANCE RESTRAINTS
; None (see manual)

; OUTPUT FLAGS
nstxout                = 100
nstvout                = 0
nstlog                 = 100
nstenergy              = 0
nstxtcout              = 5000

could you help me to make this pulling work?

Ty,

2

Hello,

are you sure you are having no problems? Why use -maxwarn 4? Do you get any warnings from grompp?

3

You have pull_start=yes and set the starting offset to the starting distance. Thus, as you can see in your output, the initial reference distance is double of what you want. Likely the system explodes and ends up in a near infinite PBC loop (this last issue has been fixed in the 2024 release, so you now get a nice error).

So set pull_start=no or pull_coord_init=0

4

Ok.
Your advide is worked!
Thank you.

I have other problems now, but I’m working on fixing them.

Ty