[gmx-users] pulling simulation

[Justin Lemkul]

On 2/13/16 10:24 AM, Mehrnoosh Hazrati 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.

If grompp is warning you about problems or inconsistencies, don't just plow 
ahead.  It's trying to tell you that you're doing something either physically or 
algorithmically nonsensical.

>
> 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

Then my Perl script is useless to you; it's for version 5.1, which has a totally 
different syntax (gmx distance -select... rather than g_dist).  So naturally it 
returns nothing, because the commands it's calling don't exist.

-Justin

>
>
> 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
>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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