[gmx-users] setting up a pull vec

[abhisek Mondal]

Hi,

What is actually happening in this error ? No consolidated reference is
available regarding this.

Fatal error:
Distance between pull groups 1 and 2 (5.851644 nm) is larger than 0.49
times the box size (4.942940) !!!

I had used cubic box with -d 2.0. Trying to do distance pulling with it.
Please provide some help regarding the same.
Here's the pull code being used:
; Pull code
pull                    = yes
pull_ngroups            = 2
pull_ncoords            = 1
pull_group1_name        = Protein_chain_A
pull_group2_name        = JZ4
pull_coord1_type        = umbrella      ; harmonic biasing force
pull_coord1_geometry    = distance      ; simple distance increase
pull_coord1_dim = N Y Y
pull_coord1_groups      = 1 2
pull_coord1_rate        = 0.00001          ; 0.00001 nm per ps = 1 nm per ns
pull_coord1_init = 0
pull_coord1_k           = 1000           ; kJ mol^-1 nm^-2
pull_coord1_start       = yes           ; define initial COM distance > 0

How large box am I to use ? I'm trying to pull a ligand from bound protein.
How much pulling it could have required ?

Please make it little bit clear, things are way too hazy.

Thank you.

On Sat, Nov 26, 2016 at 7:19 PM, abhisek Mondal <abhisek.mndl at gmail.com>
wrote:

> 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*
>> --
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>
>
>
> --
> Abhisek Mondal
>
> *Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
>



-- 
Abhisek Mondal

*Research Fellow*

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

*Kolkata 700032*

*INDIA*