[gmx-users] Umbrella sampling

[rose rahmani]

Hello;

I took 2000 configuration from trajconv. Amino acid is in its normal shape
till almost conf1000.gro(and a little more). But in for example
conf1300.gro amino acid was disintegrated. What does it mean? Would you
please help me?

Best regards
Rose

On Sun, Nov 26, 2017 at 12:39 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/25/17 3:59 PM, rose rahmani wrote:
>
>> On Sat, Nov 25, 2017 at 11:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>> On 11/25/17 3:07 PM, rose rahmani wrote:
>>>
>>> Oh sorry this is .mdp file:
>>>>
>>>> DEFINE                   = -DPOSRES
>>>>
>>>> What are you restraining? This seems counterproductive, and by default
>>>
>>>> (unless you've hacked the topology), this is going to restrain your
>>>> protein, which is definitely wrong.
>>>>
>>> yes, protein.you mean i should remove it and don't restraint anything?
>>> and
>>> for npt(previous step) run too?
>>>
>>
> What is the purpose of a restraint? To prevent motion. What is your
> objective? To cause motion of your protein towards a surface. Does it make
> sense to restrain the protein during this process?
>
> Equilibration is a separate matter.
>
> 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
>>>>
>>>> Again, I am suspicious of these cutoffs. What force field are you using?
>>>
>>> AMBER99
>>>
>>
> Then yes, those cutoffs are wrong. This is also a very old force field,
> and newer/better variants of it exist. Refer to the literature to find the
> right cutoffs for the parameter set you decide upon. This is not a trivial
> matter.
>
>
> 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 ZnO ZnO
>>>> energygrps               = SOL WAL ZnO 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-H
>>>>
>>>> You can probably just use the whole protein here, though I doubt it
>>> makes
>>> much difference.
>>>
>>> pull_coord1_type        = umbrella      ; harmonic biasing force
>>>
>>>> pull_coord1_geometry    = distance      ; simple distance increase
>>>> pull_coord1_groups      = 1 2
>>>> pull_coord1_dim         = N N Y
>>>> pull_coord1_rate        = 0.001
>>>>
>>>> Here's your problem. With a positive pull rate, you are instructing
>>> mdrun
>>>
>>>> to increase the COM distance between the protein and the ZnS surface. If
>>>> you want them to come closer, you need a negative value here, to
>>>> decrease
>>>> the distance as a function of time. Of course, this all goes out the
>>>> window
>>>> if your protein is restrained, as suggested above.
>>>>
>>>
>>> oh, i've got it.
>> you restrained chain B in tutorial but i shouldn't because ZnS is freezed?
>>
>
> No, I restrained a chain in my protein to mimic the stability of
> (physiologically) much larger systems. People typically fail to read my
> paper that is the basis of that tutorial, in which this concept is
> explained. Perhaps I need to add a bold, flashing warning that people
> should not be blindly following the method.
>
> -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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>