[gmx-users] pulling simulation

[Mehrnoosh Hazrati]

I see.

Thank you dear Justin.

Best regards,
Mehrnoosh

On Sat, Feb 13, 2016 at 6:54 PM, Mehrnoosh Hazrati <
mehrnoosh.hazrati at modares.ac.ir> wrote:

> Dear all,
>
> I'm trying to do umbrella sampling. But after running "perl distances.pl",
> I get a "summary_distances.dat file which has NO distances! Before, I get
> an error "pull reference distance for group 1 is negative" while I run
> grompp and then mdrun for pulling simulation.
>
> Below is my pull_md.mdp file.
>
> Thank you for any help and suggestion.
>
> Regards
> Mehrnoosh
>
> P.S.
> I'm using gromacs v4.5.7
>
>
> pull_md.mdp file:
>
> title       = Umbrella pulling simulation
> ; Run parameters
> integrator  = md
> dt          = 0.001
> tinit       = 0
> nsteps      = 5000000    ; 5 ns
> nstcomm     = 10
> ; Output parameters
> nstxout     = 1000      ; every 10 ps
> nstvout     = 1000
> 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     = 10
> ns_type     = grid
> rlist       = 1
> rcoulomb    = 1
> rvdw        = 1
> ; 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      = V-rescale
> tc_grps     = DPPC  DRG  SOL
> tau_t       = 0.5   0.5  0.5
> ref_t       = 310   310  310
> ; Pressure coupling is on
> Pcoupl          = Parrinello-Rahman
> pcoupltype      = semiisotropic
> tau_p           = 2.0   2
> compressibility = 4.5e-5  4.5e-5
> ref_p           = 1.0 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            = umbrella
> pull_geometry   = distance
> pull_dim        = N N Y
> pull_start      = yes
> pull_ngroups    = 1
> pull_group0     = LIPID
> pull_group1     = DRUG
> pull_init1      =  0
> pull_rate1      = -0.01
> pull_k1         = 500     ; kJ mol^-1 nm^-2
> pull_nstxout    = 1000      ; every 2 ps
> pull_nstfout    = 1000      ; every 2 ps
>



-- 
*""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""*
**** Mehrnoosh Kh. Hazrati ****
**** PhD Candidate of Physical Chemistry,Tarbiat Modares University,Tehran,
Iran ****
 *** Phone : +989123436300 ***
*** Mail : mehrnoosh.hazrati at modares.ac.ir <mehrnooshhazrati at gmail.com> ***
*"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""*