Amit Choubey wrote:
It seems that i cannot figure out a way to change the absolute reference
point (Its the origin by default).
Nope. You need to set an actual group of atoms as pull_group0 for a real
reference, otherwise the reference point is always the origin.
-Justin
Amit
On
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
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
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.
Hi,
I am still not able to see the reason for the periodic distances coming into
picture.
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 kgp.a...@gmail.com wrote:
Hi,
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
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.
I think changing the absolute reference to the initial COM of the pull group
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
It seems that i cannot figure out a way to change the absolute reference
point (Its the origin by default).
Amit
On Mon, Jan 17, 2011 at 5:52 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Amit Choubey wrote:
Yes Justin i understand that. Heres what i think is going on
I dont have any
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