It can take time to read through papers. A title, link and a short
summary would be helpful to understand what the benefit would be. In
particular whether you just need information to add the functionality
for your use case or whether enough people other would use the extra
functionality you require.
On 08/31/2018 12:42 PM, Rakesh Mishra wrote:
Dear Dr. Justin
Ultimately Mark has not replied .
Can you please tell me what this peak is revealing.
hear 3' of one strand is fixed and 3' of another strand is pulled along the
helical direction of dsDNA (12 bp). using constant velocity pulling using
your
protocol of umbrella sampling (output f/t .xvg file). (My motif is to see
rupture in presence and absence of drug).
In my view sudden drop of force corresponds to breaking of all the hbonds
of both strands occurs.
Whats your view .
On Mon, Aug 27, 2018 at 12:24 PM, Rakesh Mishra <rockin...@gmail.com> wrote:
Dear Mark,
There are several experiments have been done for protein and DNA
unfolding.
Thy became pioneer in this field. That is why force should apply and
corresponding reaction
coordinates are measured . Here Gromacs login do not allow to upload
larger data.
But I can mention some paper address . If get time Please go through these
papers .
1- NATURE | VOL 421 | 23 JANUARY 2003 | www.nature.com/nature (Carlos
Bustamante*†, Zev Bryant* & Steven B. Smith†)
2- SCIENCE 1⁄7 VOL. 275 1⁄7 28 FEBRUARY 1997 (Matthias Rief, Filipp
Oesterhelt, Berthold Heymann,Hermann E. Gaub )
That is why I asked about force-extension protocol. In Umbrella
sampling distance is increases linearly with the time and corresponding
force experienced by the system writes .
We still don't no that force/time which writes in .xvg file corresponds
which formula like f= k(vt-x) or something else.
There are other lot experiments regarding measurement of stability of the
DNA and protein under f/x curve.
One can see some theory paper also to see f/x like.
1- THE JOURNAL OF CHEMICAL PHYSICS 148, 215105 (2018)
Note- According to Justin one can write that protocol. If suppose we
write that protocol, then how to apply in gromacs.
There are only input .mdp files. We didn't know where to built the force
subroutine in .ff (force field ) directory. or somewhere else.
Hoping for response.
On Mon, Aug 13, 2018 at 6:14 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:
Hi,
Can you please share a link to something that indicates why this would be
a
good tool for modeling such experimental pulling scenarios? Making the
case
for implementing such a feature would benefit from that.
Mark
On Mon, Aug 13, 2018, 13:42 Rakesh Mishra <rockin...@gmail.com> wrote:
Hello Mark,
Thank for your clarification. Gromacs pulling has simple protocol for
pulling
using umbrella sampling. Where one can only get f/t and x/t . here t is
linearly
increases for both cases of force and distance. That actually not full
fill
the need of
experimental pulling.
On Mon, Aug 13, 2018 at 3:26 PM Mark Abraham <mark.j.abra...@gmail.com>
wrote:
Hi,
It's possible, but there is no code written for it.
Mark
On Mon, Aug 13, 2018, 12:47 Rakesh Mishra <rockin...@gmail.com>
wrote:
Dear Justin.
Thanks for your kind advise.
But why don't it is not possible to apply the constant force which
should
increases linearly (at each instant of time delta)
like at
t1 -f1
t2-f2
.
.
tn-fn
and corresponding to that force we get extension for each increment
of
time in Gromacs. This is more relevant in order to map
experimental work of unzipping or axial pulling of nucleic acid like
DNA/RNA/protein. Is it possible to build this protocol in Gromacs.
On Thu, Aug 9, 2018 at 5:30 PM Justin Lemkul <jalem...@vt.edu>
wrote:
On 8/9/18 6:37 AM, Rakesh Mishra wrote:
Dear all,
Can anyone shed some light as ,Is it possible to apply
force/time
for
pulling in gromacs. Means I want to pull my system in step wise
.
eg.
0 - t1 force applied f1
t1+dt to t2 force f2
t2+dt to t3 force f3
.
.
.
tn-1 +dt to tn force fn
Is it possible.
Not in a single run. You would have to run a simulation for
interval
0
-
dt, generate a new .tpr file for the time period of (t1+dt) - t2,
e
<https://maps.google.com/?q=le+for+the+time+period+of+(t1%2B
dt)+-+t2,+e&entry=gmail&source=g>
tc.
-Justin
--
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Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
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http://www.thelemkullab.com
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