[gmx-users] umbrella sampling

[rose rahmani]

On Mon, Nov 27, 2017 at 2:30 AM, rose rahmani <rose.rhmn93 at gmail.com> wrote:

>
>
> 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.
>>
>>> But i choose ( by pull_coord1_dim) Z direction for pulling (12 nm not
>>> 4nm), it doesn't mean that protein should just get closer to ZnS(sheet) in
>>> Z direction?
>>
>>  thank you so much
>>
>>
>>
>> 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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