Hi all,
I have problem ruunning NVT with Z direction extended to get surface
tension of a polymer packed in a cell. I tried the same procedure for an
alkane and NVT works well however for the polymer the run crashes at the
very first step..
Doe anyone have clue what wrong could be? Many
Hi Vitaly,
To get surface tension one needs to extend Z to get a surface. From bulk it
is not possible to create a surface.
My problem is NVT crashes at step 0 and no energies or any other output
file is written...
On 5 April 2013 10:25, Dr. Vitaly Chaban vvcha...@gmail.com wrote:
Hi all,
My problem is NVT crashes at step 0 and no energies or any other output
file is written...
What about visualizing your interface?
On 5 April 2013 10:25, Dr. Vitaly Chaban vvcha...@gmail.com wrote:
Hi all,
I have problem ruunning NVT with Z direction extended to get surface
But you have conf.gro
On Fri, Apr 5, 2013 at 10:29 PM, Elisabeth katesed...@gmail.com wrote:
Well I am not getting the trajectory. Simulation crashes before any step
is calculated :(
On 5 April 2013 11:20, Dr. Vitaly Chaban vvcha...@gmail.com wrote:
My problem is NVT crashes at step 0
The structure is taken from the end of previous simulation which terminates
successfully. The initial structure should not be the problem. What I do
only edit the last line (Z direction) of this structure to create vacuum.
This the output from log file.
Charge group distribution at step 0: 81
Dear Elisabeth,
I'm going to make some general remarks on what I would consider a
reasonable set of choices for such simulations:
(1) 3x3 nm in the xy plane seems perfectly fine to me if your model systems
is made up of some well-behaved molecular liquid, alkanes for instance.
(2) GROMACS
Dear Elisabeth,
PBC are still there when you increase the box length in one direction, but that
increase creates an empty region between the periodic images. provided the
empty region is large enough (larger than cutoff values, for
instance), periodicity
no longer affects the system during a
Dear Elisabeth,
actually, it is the other way around, you need increase the box length in
one direction, thus keeping periodic boundary conditions in the other two
directions while a (infinitely periodic) surface is created. and notice that
using genconf with -nbox 3 3 1 will increase your system
Dear Andre,
Thanks for the helpful information.
I need to do some text reading to understand the periodic BC effect you are
talking about. I dont see why increasing length in z direction does not lead
to periodic BC in z and only for x, y ? does that mean the thickness of
layer would be the Z
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