[gmx-users] umbrella sampling

[rose rahmani]

On Mon, Nov 27, 2017 at 1:55 AM, Alex <alexanderwien2k at gmail.com> wrote:

> 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
>
>> I've got it.
>
> would you please answer to another questions too? thank you in advance
>
>

>
>
> 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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