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

[Justin Lemkul]

On 12/12/12 5:26 PM, Justin Lemkul wrote:
>
>
> 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

and also...

3. your index.ndx file

-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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