The jump is much smaller though, and seems to decrease as I do more
continuation.
These tripeptide simulations all use the same mdp file, without the shift
potential, and with those ultra-conservative settings.
http://oi57.tinypic.com/15f2mx1.jpg
The order of restarts:
Black -> Red -> Green -> B
This seems to have nothing to do with shifted potentials or gpu.
I run a tripeptide double precisiion NVE simulation on a machine with xeon
cpu and without gpu. kill it, then continue it with the cpt file generated.
That energy jump still exists.
On Tue, Nov 11, 2014 at 1:39 PM, Johnny Lu wrote:
Going from non-shift to shifted potential changes the energy. So I was not
surprised by the sudden jump of energy between step 0 and step 10 for the
previous simulation (npt14).
But the jump near step 0 for the current simulation (npt15) is not right.
This is an equilibration run.
I have just up
On Tue, Nov 11, 2014 at 3:38 PM, Johnny Lu wrote:
> Hi.
>
> I ran 30ns NPT with Potential-shift-Verlet on both potentials, continuing
> from a NPT without Potential-shift-Verlet. The energy dropped from -3e5 to
> -4e5, which is fine.
>
> After that, I continue the 30ns NPT with the same mdp file,
The system has 30k water and a protein with ~170 amino acid.
Here are the PME tuning:
npt14:
DD step 4 load imb.: force 58.1%
step 10: timed with pme grid 80 80 80, coulomb cutoff 1.000: 37.1 M-cycles
step 20: timed with pme grid 64 64 64, coulomb cutoff 1.173: 32.6 M-cycles
step 30: timed
by the way, the machine has 4 Tesla K40m gpu, 32 xeon cpu with avx, and i
ran: nohup ../../mdrun -deffnm npt15 -cpt 1 -cpnum &
On Tue, Nov 11, 2014 at 9:38 AM, Johnny Lu wrote:
> Hi.
>
> I ran 30ns NPT with Potential-shift-Verlet on both potentials, continuing
> from a NPT without Potential-shif
Hi.
I ran 30ns NPT with Potential-shift-Verlet on both potentials, continuing
from a NPT without Potential-shift-Verlet. The energy dropped from -3e5 to
-4e5, which is fine.
After that, I continue the 30ns NPT with the same mdp file, except with a
longer run time (300ns).
The total energy was -4
