[gmx-users] umbrella sampling

[Alex]

Hi,

The answer is clearly in the error, just read it please:
2.848793 > 0.49 * (4/2) where 4 is the box length.

You can either keep the “pull_coord1_geometry    = distance” and increase
the box length or change the “pull_coord1_geometry” to  “=
direction-periodic“. I prefer the former though.

Cheers,
Alex

On Sun, Nov 26, 2017 at 23:10 rose rahmani <rose.rhmn93 at gmail.com> wrote:

> Hi;
>
> This is md_pull.mdp
>
> integrator               = md
> dt                       = 0.001
> nsteps                   = 2000000
> nstxout                  = 0
> nstvout                  = 0
> nstfout                  = 0
> nstlog                   = 500
> nstenergy                = 1000
> nstxtcout                = 1000
> rlist                    = 1.5
> rcoulomb                 = 1.5
> rvdw                     = 1.2
> coulombtype              = pme
> cutoff-scheme            = group
> vdwtype                  = Switch
> rvdw_switch              = 1.0
> pcoupl                   = no
> gen-vel                  = yes
> gen-temp                 = 0
> gen-seed                 = 173529
> constraints              = h-bonds
> pbc                      = xy
> freezegrps               = WAL ZnS
> freezedim                = Y Y Y Y Y Y
> energygrp-excl           = WAL WAL ZnS ZnS
> energygrps               = SOL WAL ZnS Protein NA CL
> 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                    = yes
> pull_ngroups            = 2
> pull_ncoords            = 1
> pull_group1_name        = ZnS
> pull_group2_name        = Protein
> pull_coord1_type        = umbrella
> pull_coord1_geometry    = distance
> pull_coord1_groups      = 1 2
> pull__coord1_dim                = N N Y
> pull_coord1_rate              = -0.001        ; 1 nm per  ns
> pull_coord1_k                 = 5000
> pull_coord1_start              = yes
>
> Program gmx grompp, VERSION 5.1.4
>
> Fatal error:
> Distance between pull groups 1 and 2 (2.848793 nm) is larger than 0.49
> times the box size (2.000000).
> You might want to consider using "pull-geometry = direction-periodic"
> instead.
>
> the box size is= 4 4 12
>
> could you please help me to resolve it?
> -----
> Mr.Lemkul told me rcutt-off is wrong and
>
>  i should'nt put "cutoff-scheme            = group" >>>but when i remove
> it i'll get  this error too;
>
>   >>With Verlet lists rcoulomb!=rvdw is not supported
>
> i know it's wrong solution but what is my alternative?!!
>
> ------
> -dummy particle should move towards the surface with a constant speed of 1
> nm/ns from z = 2 nm to z = 0 and drags the CM by the harmonic force
> corresponding to the spring constant of 5000.
>
> I DON'T know how should i implement deltaZ(=2)? which .mdp option refers to
> it?!
>
> thank you so much
>
> Best regards
> Rose
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