[gmx-users] Rupture force definition

[Rakesh Mishra]

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.


thanks



On Tue, Jan 23, 2018 at 5:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/23/18 3:01 AM, Rakesh Mishra wrote:
>
>> Ok, thanks for learifivcation.
>> Dear Justin I have one  another query regarding
>> pulling using umbrella sampling. See these two lines below.
>>
>> Eg.    Pull group   natoms    pbc atom  distance at start    reference at
>> t=0
>>                       1        31       1387
>>                       2        31       686                7.424 nm
>> 7.424 nm
>>
>> When we use grompp for obtaining .tpr file before mdrun of pulling. We see
>> 2 lines which are shown just above .
>>
>> My query is that why it is written 7.424 nm in the second line below the
>> distance at start (written in the first line).
>> I am asking because, in my thinking my object( reference group ) is very
>> close to wall ( nearly 2 nm away from the wall of yz. here I am
>> pulling in + x direction), which I can see in VMD.  Does this distance is
>> distance from the pull group to the reference group or
>> distance between pulled group to the wall near the reference group.
>>
>>
> grompp is reporting the distance that it finds along the reaction
> coordinate (first value) and the expected reference value from your .mdp
> settings (second value). However you have your groups and pull settings
> defined leads grompp to tell you that this coordinate file has a 7.4-nm
> separation between your two groups.
>
>
> -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
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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*