[gmx-users] Rupture force definition
rockinbhu at gmail.com
Wed Jan 24 11:02:58 CET 2018
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 = 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
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
"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.
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
>> 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 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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* Rakesh Kumar Mishra*
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*E-mail - rakesh.mishra at saha.ac.in <rakesh.mishra at saha.ac.in> *
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