[gmx-users] huge center of mass distance mismatch in umbrella sampling

[Justin Lemkul]

On 1/22/18 11:09 AM, Irem Altan wrote:
> Hi,
>
>
> I checked the trajectories of a few of the individual windows, and didn't see any reorientation. There is no reorientation in the pull simulation itself either, and the center of mass distances from each snapshot from the pull simulation seem to be calculated correctly. The center of mass distance is about 5.3 nm.
>
>
> I checked the center of mass distance within a trajectory (of one window) with the distances.pl script available in your tutorial, which essentially does:
>
>
> echo com of group \"Chain_A\" plus com of group \"Chain_B\" | gmx distance -s umbrella0.tpr -f conf${i}.gro -n index.ndx -oall dist${i}.xvg -select &>/dev/null
>
>
> and the center of mass seems to be around 5.3 nm for each snapshot in that trajectory.
>
>
> The .mdp file for each window is as follows:
>
>
> title       = Umbrella pulling simulation
>
> define      = -DPOSRES_bb_B -DPOSRES_bb_A
>
> ; Run parameters
>
> integrator  = md
>
> dt          = 0.002
>
> tinit       = 0
>
> nsteps      = 10000000   ; 20 ns
>
> nstcomm     = 10
>
> ; Output parameters
>
> nstxout     = 5000     ; every 100 ps
>
> nstvout     = 5000
>
> nstfout     = 5000
>
> nstxtcout   = 5000 ; every 10 ps
>
> nstenergy   = 5000
>
> ; Bond parameters
>
> constraint_algorithm    = lincs
>
> constraints             = all-bonds
>
> continuation            = yes
>
> ; Single-range cutoff scheme
>
> cutoff-scheme = Verlet
>
> nstlist     = 5
>
> ns_type     = grid
>
> rlist       = 1.4
>
> rcoulomb    = 1.4
>
> rvdw        = 1.4
>
> ; PME electrostatics parameters
>
> coulombtype     = PME
>
> fourierspacing  = 0.12
>
> fourier_nx      = 0
>
> fourier_ny      = 0
>
> fourier_nz      = 0
>
> pme_order = 4
>
> ewald_rtol = 1e-5
>
> optimize_fft    = yes
>
> ; Berendsen temperature coupling is on in two groups
>
> Tcoupl      = Nose-Hoover
>
> tc_grps     = Protein   Non-Protein
>
> tau_t       = 0.5 0.5
>
> ref_t       = 310 310
>
> ; Pressure coupling is on
>
> Pcoupl          = Parrinello-Rahman
>
> pcoupltype = isotropic
>
> tau_p           = 1.0
>
> compressibility = 4.5e-5
>
> ref_p           = 1.0
>
> refcoord_scaling = com
>
> ; Generate velocities is off
>
> gen_vel     = no
>
> ; Periodic boundary conditions are on in all directions
>
> pbc     = xyz
>
> ; Long-range dispersion correction
>
> DispCorr    = EnerPres
>
> ; Pull code
>
> pull                    = yes
>
> pull_ngroups            = 2
>
> pull_ncoords            = 1
>
> pull_group1_name        = Chain_B
>
> pull_group2_name        = Chain_A
>
> pull_coord1_type        = umbrella ; harmonic biasing force
>
> pull_coord1_geometry    = distance ; simple distance increase
>
> pull_coord1_groups = 1 2
>
> pull_coord1_dim         = N N Y

gmx distance is reporting the total COM distance between the two. The 
PMF is being computed only along the z-axis, which is the direction of 
your biasing potential. So the reaction coordinate reflects the 
component of the COM only along that axis.

-Justin

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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