On 6/17/14, 10:32 AM, Chetan Mahajan wrote:
Any ideas :
1. why slab is moving despite of position constraints?
Restraints are biasing potentials; they don't prevent movement. Why is it
necessary that your slab not move?
2. That too, only with "com" option of refcoord scaling...with "all" option
slab does not move...
Using "all" means the restraint reference for each atom is the original position
in the input coordinates, with respect to every atom individually. It is more
stringent, though it can often be unstable. The "com" option means the
restraint potential is calculated with respect to the COM of the group of
restrained atoms; it is a bit more forgiving, since the COM might only move
slightly, even if there are relatively larger changes in the individual atomic
positions.
-Justin
Thanks
On Sun, Jun 15, 2014 at 7:02 PM, Chetan Mahajan <chetanv...@gmail.com>
wrote:
The pics should be seen in the reverse order. Due to sorting by name,
"After equilibration" pic occurs first.
On Sun, Jun 15, 2014 at 6:54 PM, Chetan Mahajan <chetanv...@gmail.com>
wrote:
Thanks.
No, same things do not happen when it's a NVT simulation or no mixed
potentials. Also, with mixed potentials in NPT simulation, this things of
slab moving in one direction (thus following water movement) happens only
with -com option of refcoord-scaling, *not with -all option for
refcoord-scaling. *
I have a crystal slab with equal amount of water on both the sides.
During NPT equilibration (with refcoord-scaling option of -com, not -all),
some water on side side of the slab enters opposite side due to periodic
boundary conditions I have (say water on the right side of the slab,
crosses boundary of the box and enter the left side of the slab due to
periodic boundaries. Even crystal slab follows this water and move same
distance in the same direction of water movement. Following link shares
pictures of the solvated slab before and after equilibration:
https://www.dropbox.com/sh/tjq80jgnff1y7ur/AAAzhnv8uwl-UMQ0TYx8PuPAa
I feel, this is not an error, but it is odd. Due to periodicity we have,
output of any calculations will remain the same. Again, with -all option
for refcoord scaling, this movement of water and slab DOES NOT occur.
Thanks a lot!
regards
Chetan
On Sat, Jun 14, 2014 at 4:40 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:
Hi,
Repeating myself - simplify things! Do sane things happen with NVT? With
no
mixed potentials?
Your words aren't making sense to me - you'll do much better with
pictures,
making sure you turn on your visualizer's option to show the periodic
box.
Mark
On Fri, Jun 13, 2014 at 8:45 PM, Chetan Mahajan <chetanv...@gmail.com>
wrote:
Hi Justin,
I, actually, do not want to preserve any voids. Initial void that I
mentioned is supposed to be filled by water during equilibration and it
does so. However, problem is that some or major quantity of water
moves out
from one side of the box to enter from the opposite side (obeying
periodic
boundary conditions) and crystal slab moving following water movement.
Thus
although initially there is almost equal amount of water on both sides
of
the slab, we have more water on one side of the slab than the other
side
after equilibration. In other words, length of the box on one side of
the
slab is more than the other side after equilibration, although it is
same
on both sides before equilibration. My dilemma is whether this is due
to
pressure coupling or any gromacs thing or due to potentials (mixed
buckingham and LJ)?
Thanks
Chetan
On Fri, Jun 13, 2014 at 7:43 AM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 6/12/14, 11:15 PM, Chetan Mahajan wrote:
Dear All,
I am simulating TiO2 crystal solvated by water and ions like
sodium and
formate. I am observing one peculiar thing, and I would like to
rectify
that. I have initial structure of crystal slab at the center of the
box
elongated in z-direction and almost equal boxlength on both the
sides,
with
a gap of 1 nm between slab surface and first layer of water close to
slab.
This space is kept to avoid water going on the sides of the
crystal
during
equilibration. This was a minor information. Now, the main
observation
is
that during NPT equilibration, water from one side of the slab
enters
the
other opposite side of the slab (using periodic conditions) so that
boxlengths on both sides of the slab are very different at the end
of
equilibration. Is this an artifact of pressure coupling? Following
is my
equilibration .mdp file. I have tried varying the compressibility
and
tau-p
parameters in the following file. e.g. zero compressibility in x/y
direction or tau-p reduced to 3.
With pressure coupling, any voids present in the system will be
compressed. If you need to try to preserve some sort of vacuum
layers,
use
NVT.
-Justin
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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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