[gmx-users] setting up a pull vec

[abhisek Mondal]

Hello Christopher,

I have restrained the protein chain and ligand during previous NPT
equilibration step(10ns). Is it still possible that the structure will
scatter all over if we start pulling ?

I want to pull the ligand out of the binding site of this protein and
collect intermediary conformers during the process to study the concerned
structural changes. Please give me some advice regarding the process.

Thanks.



On Sat, Nov 26, 2016 at 8:04 AM, Christopher Neale <
chris.neale at alum.utoronto.ca> wrote:

> You haven't told us what you want to do, but perhaps you want to pull them
> apart along the vector that connects the centers of mass of these two
> species. One possible way to do that is to use gmx traj -com to get the two
> centers of mass, then figure out the vector yourself. That's going to get
> messy if the whole complex tumbles in solution, so you could also add a few
> absolute position restraints to pin down one of the molecules.
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of abhisek
> Mondal <abhisek.mndl at gmail.com>
> Sent: 25 November 2016 02:37:18
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] setting up a pull vec
>
> Hi,
>
> I'm trying to run a umbrella sampling using following pull code:
> ; Pull code
> pull                    = yes
> pull_ngroups            = 2
> pull_ncoords            = 1
> pull_group1_name        = JZ4
> pull_group2_name        = Protein_chain_A
> pull_coord1_type        = umbrella      ; harmonic biasing force
> pull_coord1_geometry    = direction-periodic
> pull_coord1_groups      = 1 2
> pull_coord1_dim         = Y Y Y ; pulling in all dimension
> pull_coord1_rate        = 0.01          ; 0.01 nm per ps = 10 nm per ns
> pull_coord1_k           = 500           ; kJ mol^-1 nm^-2
> pull_coord1_start       = yes           ; define initial COM distance > 0
>
> This approach needs me to specify a pulling vec which is essentially not
> 0,0,0.
>
> Could you please suggest me a way to decide how to provide the pull vec ?
>
> Thanks.
>
> --
> Abhisek Mondal
>
> *Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
> --
> 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.
>



-- 
Abhisek Mondal

*Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*