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

[Irem Altan]

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

pull_coord1_rate        = 0.0

pull_coord1_k           = 5000          ; kJ mol^-1 nm^-2

pull_coord1_start = yes           ; define initial COM distance > 0

pull_nstxout    = 1000      ; every 2 ps

pull_nstfout    = 1000      ; every 2 ps

where -DPOSRES_bb_B -DPOSRES_bb_A define restraints for 4 C_alphas on each chain to prevent them from rotating.

The reaction coordinate is about 4 nm (from 5.3 to 9.3 nm), but I ran simulations up to 7.3 nm. I'm pulling in the z direction, and the box length in that direction is 19.5 nm. (But anyway Gromacs would stop the simulation if I pull longer than half the size of the box.)

I should also note that I use more or less this setup for the same protein for different interfaces and do not encounter such a problem.

Best,
Irem
________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Monday, January 22, 2018 7:50:29 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] huge center of mass distance mismatch in umbrella sampling



On 1/21/18 6:53 PM, Irem Altan wrote:
> Hi,
>
>
> I have two copies of a protein that are in contact with each other. Their center of mass distance is about 5.5 nm. However, in the resulting potential of mean force, there is an energetic minimum at 3.5 nm. How is this at all possible? At that distance half of the protein would be overlapping each other. How could I diagnose why this is happening?

Watch the trajectory from that window. Have the proteins reoriented?
What was the initial COM distance, and how long was the reaction
coordinate? What are your .mdp settings?

-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
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.biochem.vt.edu_people_faculty_JustinLemkul.html&d=DwICAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=UiH5zve1AFInQlFAVuh-CFdEKls6Ovle_wT_BBO91Cg&s=ANRiAcIDHeYM3DO61dtuxG07a8O5QxtOC_37HP2IJ5E&e=

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

--
Gromacs Users mailing list

* Please search the archive at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists_GMX-2DUsers-5FList&d=DwICAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=UiH5zve1AFInQlFAVuh-CFdEKls6Ovle_wT_BBO91Cg&s=YuHxO2nbQ53Sq0BOgK-IsYXyRukM6tcVGeqR5nYHOcE&e=  before posting!

* Can't post? Read https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists&d=DwICAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=UiH5zve1AFInQlFAVuh-CFdEKls6Ovle_wT_BBO91Cg&s=DBffryLETPbG5J5p4g4xrm_rk3TDJ1G-DpkhZy4pOEA&e=

* For (un)subscribe requests visit
https://urldefense.proofpoint.com/v2/url?u=https-3A__maillist.sys.kth.se_mailman_listinfo_gromacs.org-5Fgmx-2Dusers&d=DwICAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=UiH5zve1AFInQlFAVuh-CFdEKls6Ovle_wT_BBO91Cg&s=69Qr1E1ytSelqgPGedgOdHsLL5DjgdZOlUD2T6e_AQM&e=  or send a mail to gmx-users-request at gromacs.org.