There is no such thing as "out of the box". You are looking at an
arbitary visual representation of the system.
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
https://twitter.com/dr_dbw/status/909559339366572032
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposit
It likely in nvt you used constraint so your structure is not so much
different from initial,
In NPT you removed constraint.
When you visualize or analyze result, you need remove boundary condition as
Justin said above
On Tue, May 15, 2018, 07:43 Dhumal, Nilesh wrote:
> Hello Users,
>
>
> I am r
On 5/15/18 3:26 PM, Irem Altan wrote:
Hi,
I ran a simulation using GPUs, and now I would like to calculate the energy
between two protein chains, as well as energy between the protein and the
solvent. For this, I am trying to run enemat:
gmx enemat -f umbrella0.edr
but this fails:
Opened
Hi,
I ran a simulation using GPUs, and now I would like to calculate the energy
between two protein chains, as well as energy between the protein and the
solvent. For this, I am trying to run enemat:
gmx enemat -f umbrella0.edr
but this fails:
Opened umbrella0.edr as single precision energy f
Thank you,
it worked.
On Mon, May 14, 2018 at 3:43 PM, Mark Abraham
wrote:
> Hi,
>
> I don't know whether solvate supports such boxes, but if it does I would
> use editconf first to describe the box, and then solvate to fill it.
> Currently you are filling a cubic box and then transforming it to
Hi Dr. Warren,
You're right - the water does fill up the entire space when neighboring
images are turned on.
By reading online, I learned that it is okay if molecules seem to move away
from the box during the simulation and the visualization can be fixed
through the use of 'trjconv', but is it ok
On 5/15/18 2:46 AM, Rakesh Mishra wrote:
Dear Justin,
In all the respect that you have suggested is absolutely correct.
But I have a question that just like a constant rate pulling
like - [pull_coord1_rate= 0.01 ; 0.01 nm per ps = 10 nm
per 1 ns ( which was from your umbrell
