On 8/8/13 11:51 AM, Brad Van Oosten wrote:
FYI I have done some more experimenting on the problem with different
versions and computers running the exact same start .tpr file and this is
what ive found:
Computer A with 4.6.1 or 4.6.3 with MPI = random energy drops
Computer A with 4.6.1 or 4.6.
FYI I have done some more experimenting on the problem with different
versions and computers running the exact same start .tpr file and this is
what ive found:
Computer A with 4.6.1 or 4.6.3 with MPI = random energy drops
Computer A with 4.6.1 or 4.6.3 without MPI = no random energy drops
Compute
On 8/1/13 5:18 PM, Brad Van Oosten wrote:
To be honest, i have not updated that box to the newest version. If it
appears to be a serious bug i could do it and rerun these sims to see if it
does persist.
I think it is worth doing. If -rerun calculates sensible energies but the
original sim
To be honest, i have not updated that box to the newest version. If it
appears to be a serious bug i could do it and rerun these sims to see if it
does persist.
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Sent from the GRO
On 8/1/13 5:08 PM, Brad Van Oosten wrote:
This was done on v 4.6.1
Does the same problem persist in 4.6.3?
-Justin
md50.mdp:
title= MD simulation
integrator = md ; MD integrator
tinit= 0
dt = 0
This was done on v 4.6.1
md50.mdp:
title= MD simulation
integrator = md ; MD integrator
tinit= 0
dt = 0.002; 2 fs timestep
nsteps = 5000 ; Number of st
On 8/1/13 4:58 PM, Brad Van Oosten wrote:
I used the mdrun -rerun option to recalculate the energies of the system and
it gave me nearly the same energy plot but without the random drops(see plot
below). I am still unsure what is causing the jumps but i do not believe it
is from my system. Si
I used the mdrun -rerun option to recalculate the energies of the system and
it gave me nearly the same energy plot but without the random drops(see plot
below). I am still unsure what is causing the jumps but i do not believe it
is from my system. Since the energy is used in the calculation for
On 7/31/13 4:45 PM, Brad Van Oosten wrote:
looking at the first 2 peaks, they are created from single outlying points in
the trajectory. Visually, I can see no discernible difference between it and
the frame before/after with the higher energy.
To find the source, you'll probably have to fur
looking at the first 2 peaks, they are created from single outlying points in
the trajectory. Visually, I can see no discernible difference between it and
the frame before/after with the higher energy.
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