On 6/17/14, 5:20 PM, Chetan Mahajan wrote:
Thanks, Justin. That makes it clear. I have one small question: I do not
know how does position restraint algorithm work with other things in
gromacs, but doesn't it generate a lot of stress due to slab moving from
center to near box boundary despite
Any ideas :
1. why slab is moving despite of position constraints?
2. That too, only with com option of refcoord scaling...with all option
slab does not move...
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.
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
Thanks, Justin. That makes it clear. I have one small question: I do not
know how does position restraint algorithm work with other things in
gromacs, but doesn't it generate a lot of stress due to slab moving from
center to near box boundary despite of position restraints, when -com
option is
*Forgot to comment:*
*So you are saying: because it is more forgiving, we are observing slab
movement in a run with com option for refcoord scaling, and NOT in all
option...as such, choosing any one of options com or all for refcoord
scaling should not matter simulation results point of view,
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
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
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
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
Other main observation is that crystal slab following water, moving in the
same direction, *despite of position restraints (refcoord-scaling=com
option). *
Thanks
Chetan
On Fri, Jun 13, 2014 at 1:45 PM, Chetan Mahajan chetanv...@gmail.com
wrote:
Hi Justin,
I, actually, do not want to
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