Amit Choubey wrote:
Yes Justin i understand that. Heres what i think is going on
I dont have any reference group. Now the COM distance is calculated wrt
the origin and whenever the COM is more than half of the box its causing
problem.
Correct.
I think changing the absolute reference to the initial COM of the pull
group (using pull_init1) should fix this issue but i am not confident.
Using a defined reference group is the better method. That way, the pull
distance is calculated with respect to this reference, and it sounds like that
will allow you to use the box you have already set up.
-Justin
Thanks for looking into this.
On Mon, Jan 17, 2011 at 5:36 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Amit Choubey wrote:
Hi,
I am still not able to see the reason for the periodic distances
coming into picture.
I guess I don't fully understand your procedure. If you only want
to pull to a COM separation of 15 nm, there should be no problem,
but yet you're achieving a COM separation of 18.5 nm? That's
exactly the problem. If your box is 37 nm, 18.5 nm corresponds to
the transition at which the code utilizes either the unit cell
distance or the periodic distance as the restraint distance. So it
is as this point that your forces go haywire.
-Justin
Also, why pull_geometry = direction_periodic cannot be used with
P-coupling; although it seems to do what i want.
Amit
On Mon, Jan 17, 2011 at 1:04 PM, Amit Choubey
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> wrote:
Hi,
Initially, the pull group center of mass is at 8.16 nm and i
want to
pull 15 nm. I started with a box size of 37 nm in the pull
direction.
The problem occurs when the COM is at 18.5 nm (ie at half the box
length).
Thanks for the attention.
Amit
On Mon, Jan 17, 2011 at 11:40 AM, Justin A. Lemkul
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> wrote:
Amit Choubey wrote:
Hi all,
I am trying to do pulling simulation. Following are
the pull
parameters
pull = umbrella
pull_geometry = direction
pull_vec1 = 0 0 1
pull_group1 = RNA
pull_rate1 = 0.01
pull_k1 = 1000
pull_start = yes
Everything works fine until the pull group COM
reaches half
the box length. The COM position changes by the box
length
and that causes huge force on the group. What should
i do to
fix this ? Also i am using NPT coupling.
You have to use a sufficiently large box, otherwise the
periodic
distance becomes the reference distance when this
happens. This
has been discussed numerous times on the list (hint:
there is an
archive for a reason!) and in the tutorial linked here:
http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling
-Justin
Amit
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> |
(540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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