[gmx-users] Pulling simulation

[Naveen BK]

thank you so much @Quyen Vu. I'll get back to you soon.

On Mon, Apr 8, 2019 at 7:00 PM Quyen Vu <vuqv.phys at gmail.com> wrote:

> Hi Naveen,
> I think you are looking for absolute reference position in space, which is
> mention on page 436 of manual 2019.1
> In my case, I pull ACE residue.
> my pulling code is:
> pull                    = yes
> pull_ncoords            = 1         ; only one reaction coordinate
> pull_ngroups            = 1         ; two groups defining one reaction
> coordinate
> pull_coord1_groups      = 0 1
> pull_group1_name        = ACE
> pull_coord1_type        = umbrella  ; harmonic potential
> pull_coord1_geometry    = direction ; simple distance increase
> pull-coord1-vec         = 1.0 0.0 0.0
> pull_coord1_dim         = Y N N
> pull_coord1_start       = yes       ; define initial COM distance > 0
> pull-coord1-origin      = 18.0 5.19 5.06     ; absoulte reference point
> pull_coord1_rate        = 0.005      ; 0.005 nm per ps = 5 nm per ns
> pull_coord1_k           = 600      ; kJ mol^-1 nm^-2
>
> ;*********************************************************************************
> Hope my code is useful with you or if I wrong, someone can correct me.
> Best regards,
> Quyen
>
> On Mon, Apr 8, 2019 at 8:20 AM Naveen BK <naveenbk4717 at gmail.com> wrote:
>
> > Dear all,
> >
> > This question is regarding Umbrella sampling. My group 1 is substrate and
> > group 2 protein. Trying to pull the substrate molecule from the active
> site
> > pocket. In all the cases(for group 2), I used either atom or residue for
> > the center of mass [COM]. Now I want to run a simulation by considering
> > that COM of protein which may be present in the vacuum or in the empty
> > space. In other words, I don't want to fix any atom or residue of the
> > protein but I want to fix an empty space. I was not able to find any
> > solutions regarding this if anyone could help me to figure it, would be
> > great.
> >
> > --
> > Thanks and Regards,
> > Naveen Krishna
> > +91 8123474717
> > --
> > 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.
> >
> --
> 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.
>


-- 
Regards,
Naveen Krishna
8123474717