[gmx-users] Regarding Umbrella sampling

[Amir Zeb]

Thanks Justin,

The current version I'm working on is 5.0.6, and I don't have access to
update this version. Can you please let me know how to get files compatible
for this version?

Regards!

-Amir

On Wed, Mar 8, 2017 at 5:32 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/8/17 8:11 PM, Amir Zeb wrote:
>
>> Hello gmx users,
>>
>> I want to calculate binding energy for a protein-ligand complex.
>> Obviously,
>> this is the very first time, I'm handling umbrella sampling, so I faced
>> the
>> following error.
>>
>> WARNING 2 [file pull.mdp, line 65]:
>>   Unknown left-hand 'pull_ncoords' in parameter file
>>
>>
>>
>> WARNING 3 [file pull.mdp, line 65]:
>>   Unknown left-hand 'pull_group1_name' in parameter file
>>
>>
>>
>> WARNING 4 [file pull.mdp, line 65]:
>>   Unknown left-hand 'pull_group2_name' in parameter file
>>
>>
>>
>> WARNING 5 [file pull.mdp, line 65]:
>>   Unknown left-hand 'pull_coord1_type' in parameter file
>>
>>
>>
>> WARNING 6 [file pull.mdp, line 65]:
>>   Unknown left-hand 'pull_coord1_geometry' in parameter file
>>
>>
>>
>> WARNING 7 [file pull.mdp, line 65]:
>>   Unknown left-hand 'pull_coord1_groups' in parameter file
>>
>>
>>
>> WARNING 8 [file pull.mdp, line 65]:
>>   Unknown left-hand 'pull_coord1_dim' in parameter file
>>
>>
>>
>> WARNING 9 [file pull.mdp, line 65]:
>>   Unknown left-hand 'pull_coord1_rate' in parameter file
>>
>>
>>
>> WARNING 10 [file pull.mdp, line 65]:
>>   Unknown left-hand 'pull_coord1_k' in parameter file
>>
>>
>>
>> WARNING 11 [file pull.mdp, line 65]:
>>   Unknown left-hand 'pull_coord1_start' in parameter file
>>
>>
>>
>> There was 1 note
>>
>> There were 11 warnings
>>
>>
>> *The pull.mdp file is this one:*
>>
>>
>> title       = Umbrella pulling simulation
>> define      = -DPOSRES_NAD
>> ; 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   NAD
>> 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        = NAD
>> pull_group2_name        = Protein
>> 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        = 0.01          ; 0.01 nm per ps = 10 nm per ns
>> pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2
>> pull_coord1_start       = yes           ; define initial COM distance > 0
>>
>>
>> Please let me know where I'm making the mistake.
>>
>>
> You're using an outdated version of GROMACS that does not recognize the
> new syntax that was introduced in version 5.1.
>
> -Justin
>
> --
> ==================================================
>
> 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
>
> ==================================================
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