[gmx-users] Umbrella sampling - chain A does not get pulled

[Justin Lemkul]

On 12/12/12 5:15 PM, Davide Mercadante wrote:
> Dear Justin,
>
> Thank you for your reply. To be sure I carefully ran the simulations again
> using the following .mdp file that includes the pull lines and
> -DPOSRES_B to restrain chain B from being pulled when chain A is being
> pulled (it is the .mdp file given in the tutorial):
>
> title       = Umbrella pulling simulation
> define      = -DPOSRES_B
> ; Run parameters
> integrator  = md
> dt          = 0.002
> tinit       = 0
> nsteps      = 250000    ; 500 ps
> nstcomm     = 10
> ; Output parameters
> nstxout     = 5000      ; every 10 ps
> nstvout     = 5000
> nstfout     = 500
> nstxtcout   = 500       ; every 1 ps
> nstenergy   = 500
> ; Bond parameters
> constraint_algorithm    = lincs
> constraints             = all-bonds
> continuation            = yes       ; continuing from NPT
> ; Single-range cutoff scheme
> 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
> ; 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            = umbrella
> pull_geometry   = distance  ; simple distance increase
> pull_dim        = N N Y
> pull_start      = yes       ; define initial COM distance > 0
> pull_ngroups    = 1
> pull_group0     = Chain_B
> pull_group1     = Chain_A
> pull_rate1      = 0.01      ; 0.01 nm per ps = 10 nm per ns
> pull_k1         = 1000      ; kJ mol^-1 nm^-2
>
>
> I get slightly different distances but it is still now working. From the
> load of the trajectories chain B is not getting pulled. However, after

I'm assuming you mean chain A here.  Chain B is restrained while A is pulled 
away from it.

> running the distance.pl script I get a COM distance within the range 2.3nm
> to 6.0nm). Can you please help me to understand what I am doing wrong?
>

None of this makes sense to me.  Your COM distance increases, but you say you 
can't see anything moving?  One necessitates the other.  Are you loading the 
trajectory properly?  If you're using VMD, you have to load the starting 
coordinates first and then the trajectory is loaded as data for that molecule.

> My command line is:
>
> Grompp -f pull.mdp -c after_npt.gro -p topol.top -o pull.tpr -t state.cpt
> (checkpoint file from the previous npt step) -n index.ndx (which includes
> groups 19 and 20, chains A and B respectively).
>
> Mdrun then uses pull.tpr...
>
> Please don't hesitate to ask me any other information you may need to
> figure this out. I am not sure what I am doing wrong..
>

If you still can't figure out what's going on, please send me (off list) the 
following:

1. Your summary_distances.txt file
2. Several coordinate files - conf0.gro, conf100.gro, conf200.gro, and conf500.gro

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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