[gmx-users] Rupture force definition

[Rakesh Mishra]

Thank you Justin.

I got  it and did it also.

On Thu, Jan 25, 2018 at 7:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/25/18 2:41 AM, Rakesh Mishra wrote:
>
>> Thanks for reply.
>>
>> Dear Justin
>>
>> Is it possible to transform .xtc file in the form of .pdb formate
>> excluding solvent and ion molecules simultaneously.
>> I am familiar to do this with "trjconv" command. But by using this we can
>> transform .xtc file in the form of .pdb formate,
>> where water molecules and ions gets also present in the .pdb formate. How
>> it is possible to save only system coordinates
>> rather than solvent ( water molecules ) molecules and ions  at the same
>> time .
>>
>
> trjconv (like most GROMACS tools) lets you pick whatever subset of atoms
> you want. Choose an appropriate group for output that suits your needs.
>
> -Justin
>
>
>
>>
>>
>>
>> On Wed, Jan 24, 2018 at 6:25 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>> On 1/24/18 5:02 AM, Rakesh Mishra wrote:
>>>
>>> Dear Justin
>>>>
>>>> Thank you very much  for removing the doubts .
>>>> Let me extend  my query in this respect again. As according to pull code
>>>> formate which is  discussed in your testing work of umbrella sampling .
>>>> Please have a rough look.
>>>>
>>>> Pull code
>>>> pull                    = yes
>>>> pull_ngroups            = 2
>>>> pull_ncoords            = 1
>>>> pull_group1_name        = chain_B
>>>> pull_group2_name        = chain_A
>>>> pull_coord1_type        = umbrella      ; harmonic biasing force
>>>> pull_coord1_geometry    = distance      ; simple distance increase
>>>> pull_coord1_groups      =  1 2
>>>> pull_coord1_dim         = Y N N
>>>> pull_coord1_rate        = 0.0005          ; 0.0005 nm per ps = 5 nm per
>>>> 10
>>>> ns
>>>> pull_coord1_k           = 400          ; kJ mol^-1 nm^-2
>>>> pull_coord1_start       = yes           ; define initial COM distance >
>>>> 0
>>>>
>>>> As according to some explanation on the net,  I found  that  in the Pull
>>>> code written above,
>>>>
>>>> "pull_group1_name = chain_B "   gromacs read it as a reference group by
>>>> default &
>>>> "pull_group2_name = chain_A"    gromacs read it as a pull group by
>>>> default.
>>>>
>>>> But suppose, we want to pull 2 or more groups eg.  B2 & B3 in the same
>>>> system and which are having
>>>> two respective reference group A2 & A3 w. r. t. pulled groups  B2 & B3.
>>>> Then how to define these one in above code.
>>>>
>>>> I mean If I have  A1, A2, and A3 three pull group ( which we want to
>>>> pull)
>>>> and corresponding to these we have three
>>>> reference group B1 , B2 and B3. We are pulling all in the same direction
>>>> (+x  direction ).
>>>> then how to define these simultaneously in above pull code.
>>>>
>>>> will I need to define rate for all these pull group separately ( three
>>>> times) or if rate value is same then no need to
>>>>    define three times corresponding to these three pull groups.
>>>>
>>>> You can define any number of groups to be used in any number of biasing
>>> potentials. Each needs its own complete definition (geometry, dimensions,
>>> rate, force constant, etc). Get rid of the notion of "reference" and
>>> "pull
>>> group" in this application; groups define the two ends of a reaction
>>> coordinate, nothing more.
>>>
>>>
>>> -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
>>>
>>> ==================================================
>>>
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>>>
>>
>>
> --
> ==================================================
>
> 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
>
> ==================================================
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-- 
* Rakesh Kumar Mishra*
*  (RA)CSD  SINP Kolkata, India*

*E-mail - rakesh.mishra at saha.ac.in <rakesh.mishra at saha.ac.in> *

*Phone n. +91 9473662491, +91877749632*