On Thu, Oct 30, 2014 at 12:30 PM, Ioanna Styliari
wrote:
> Thank you both for your prompt replies.
>
> Dr Vitaly Chaban: Is there any way of evaluating how many nodes are needed or
> is it just by a trial-error approach?
If your number of cores gives an error, try another number of cores.
Dr.
On 10/30/14 7:30 AM, Ioanna Styliari wrote:
Thank you both for your prompt replies.
Dr Vitaly Chaban: Is there any way of evaluating how many nodes are needed or
is it just by a trial-error approach?
If what Vitaly says is true, this would be a very sneaky bug that has not been
noticed be
Thank you both for your prompt replies.
Dr Vitaly Chaban: Is there any way of evaluating how many nodes are needed or
is it just by a trial-error approach?
Justin: Although 1fs works, I was aiming for 2fs steps in the MD but it
crashes. I was thinking to run the first 2ns with 1fs and then try
On 10/29/14 2:07 PM, Ioanna Styliari wrote:
Dear Gromacs users,
I am simulating a system that contains a drug nanoparticle in amorphous state,
surrounded by water and the water is also surrounded by acetone (imagine 2
concentric spheres for the first two inside one big box for the acetone).
I do not believe it is because of packmol or because of equilibration.
What about trying a different number of cores per job? Sometimes,
certain number of cores do not want to work correctly for certain
systems.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Wed, Oct 29, 2014 at 7:07 PM, I
Dear Gromacs users,
I am simulating a system that contains a drug nanoparticle in amorphous state,
surrounded by water and the water is also surrounded by acetone (imagine 2
concentric spheres for the first two inside one big box for the acetone).
I used to build the system using gromacs editco
