[gmx-users] Rupture force definition

[Rakesh Mishra]

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 .





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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>
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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*