[gmx-users] energy group exclusion

[rose rahmani]

Yes.
thank you so much

On Sun, Jan 14, 2018 at 7:05 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/14/18 9:59 AM, rose rahmani wrote:
>
>> Hello;
>>
>> this is md_pull.mdp
>>
>> integrator               = md
>> dt                       = 0.002
>> nsteps                   = 1000000
>> nstxout                  = 5000
>> nstvout                  = 5000
>> nstfout                  = 500
>> nstlog                   = 500
>> nstenergy                = 1000
>> nstxtcout                = 1000
>> nstlist                  = 10
>> rlist                    = 1.5
>> cutoff-scheme            = Verlet
>> energygrp-excl           = WAL WAL ZnS ZnS
>> coulombtype              = pme
>> rcoulomb                 = 1.2
>> vdwtype                  = Switch
>> rvdw_switch              = 1.0
>> rvdw                     = 1.2
>> pcoupl                   = no
>> gen_vel                  = no
>> constraints              = h-bonds
>> ns_type                  = grid
>> pbc                      = xy
>> freezegrps               = WAL ZnS
>> freezedim                = Y Y Y Y Y Y
>> energygrps               = SOL WAL ZnS Protein NA CL
>> energygrp-excl           = WAL WAL ZnS ZnS
>> nwall                    = 2
>> wall-atomtype            = C C
>> wall-type                = 9-3
>> wall-density             = 150 150
>> wall-ewald-zfac          = 3
>> ewald-geometry           = 3dc
>> fourierspacing           = 0.12
>> tcoupl                   = v-rescale
>> tc-grps                  = System
>> tau-t                    = 0.1
>> ref-t                    = 300
>>
>> ; Pull code
>> pull                    = yes
>> pull_ngroups            = 2
>> pull_ncoords            = 1
>> pull_group1_name        = ZnS
>> pull_group2_name        = Protein
>> pull_coord1_type        = umbrella
>> pull_coord1_geometry    = direction
>> pull_coord1_groups      = 1 2
>> pull_coord1_dim         = N N Y
>> pull_coord1_vec         = 0 0 1
>> pull_coord1_rate        = -0.001
>> pull_coord1_k           = 5000
>> pull_coord1_start       = yes
>> pull_nstxout            = 10
>>
>> ----------------------------------------------
>>
>> ERROR 1 [file md_pull.mdp]:
>>    Energy group exclusions are not (yet) implemented for the Verlet scheme
>>
>>
>> WARNING 1 [file md_pull.mdp]:
>>    Can not exclude the lattice Coulomb energy between energy groups
>>
>> Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
>> Calculated rlist for 1x1 atom pair-list as 1.208 nm, buffer size 0.008 nm
>> Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
>> Note that mdrun will redetermine rlist based on the actual pair-list setup
>> Calculating fourier grid dimensions for X Y Z
>> Using a fourier grid of 36x36x300, spacing 0.111 0.111 0.120
>> Pull group  natoms  pbc atom  distance at start  reference at t=0
>>         1       560       280
>>         2        26       773       1.763 nm          1.763 nm
>> Estimate for the relative computational load of the PME mesh part: 0.77
>>
>> NOTE 3 [file md_pull.mdp]:
>>    The optimal PME mesh load for parallel simulations is below 0.5
>>    and for highly parallel simulations between 0.25 and 0.33,
>>    for higher performance, increase the cut-off and the PME grid spacing.
>>
>>
>> This run will generate roughly 149 Mb of data
>>
>> There were 3 notes
>>
>> There was 1 warning
>>
>> There were 3 notes
>>
>> There was 1 warning
>>
>> -------------------------------------------------------
>> Program gmx grompp, VERSION 5.1.4
>> Source code file:
>> /home/sjalili/gromacs-5.1.4/src/gromacs/gmxpreprocess/grompp.c, line:
>> 2107
>>
>> Fatal error:
>> There was 1 error in input file(s)
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>>
>> i implemented  energygr-excl in mdp file, so why get this error?!
>>
>
> Read the above - such exclusions are not compatible with either the Verlet
> scheme or with PME.

Sorry, i couldn't understand "Read the above -such exclusions " ?

> and my second question is that i want to pull Protein(to get closer to
>> sheet) to ZnS sheet, so should i use position restraint for Protein in
>> this
>> step?
>>
>
> If you want to induce motion in some species, does it make sense to apply
> a biasing potential that prevents motion?
>
> and what is the difference between geometry= direction or distance in my
>> system?
>>
>
> Please see the manual for a description of these features.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
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