[gmx-users] energy group exclusion

[Justin Lemkul]

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.

> 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

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jalemkul at vt.edu | (540) 231-3129
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