Hi Mark,
I am using Gromacs v.2018.x and as I tested it is not the matter of using
GPU or CPU.
The issue was from my side where by mistake I had put the wall (in all
posre.x,y,z.itp) exactly on the outer box borders so that my inner box and
outer box were fully identical,
so the molecules had no l
Hi,
It's certainly conceivable that such restraints are ineffective in some run
modes. However, "on the GPU" describes a range of scenarios. If you're
running with 2019.x, does adding -bonded cpu to the mdrun command line
restore the functionality?
Otherwise, please try the "working CPU" run on a
Thanks Billy,
> If the flat bottom restraint energy is zero, then that means that the
> restraints aren't being applied, or your predefined distance is not being
> exceeded. I doubt you would get binary zero values if it was the second
> option, so something is probably wrong with your syntax or
If the flat bottom restraint energy is zero, then that means that the
restraints aren't being applied, or your predefined distance is not being
exceeded. I doubt you would get binary zero values if it was the second
option, so something is probably wrong with your syntax or your inclusion
of the r
You may want to consider using smart-bottom restraints instead?
Jokes aside, why does it matter if your molecules move into the next
periodic image?
Cheers,
Billy
On Wed., 11 Sep. 2019, 5:03 pm Alex, wrote:
> Hi,
>
> Any comment, please?
>
> Thank you.
> Alex
>
> On Mon, Sep 9, 2019 at 10:22 P
Hi,
Any comment, please?
Thank you.
Alex
On Mon, Sep 9, 2019 at 10:22 PM Alex wrote:
> Hi Mark,
>
> Thank you for your response.
> Here are the part of options that gmx energy gives me out:
>
> 9 Coulomb-(SR)10 Coul.-recip.
> 11 Flat-bottom-posres
Hi Mark,
Thank you for your response.
Here are the part of options that gmx energy gives me out:
9 Coulomb-(SR)10 Coul.-recip.
11 Flat-bottom-posres 12 Potential
13 Kinetic-En. 14 Total-Energy15 Conserved-En
Energy
Hi,
The total potential energy violating the restraints is reported, so you
should see that there is an appropriate contribution there, and probably
plan to stiffen the force constant.
Mark
On Fri., 6 Sep. 2019, 17:23 Alex, wrote:
> Dear all,
> Using the flat-bottom (K=4184 KJ/(mol. nm^2)) res
Dear all,
Using the flat-bottom (K=4184 KJ/(mol. nm^2)) restrain I tried to have a
smaller cubic box as semi-preamble walls inside a bigger cubic box so that
all molecules except water would stay inside the smaller box during the
simulation, however, the wall doesn't work and the molecules are also
