Hi Diego,
What do the color codes indicate? It looks like the energies are in replica
space and not in temperature space.
Best,
Koushik
On Wed, Aug 5, 2020 at 6:05 PM Diego Morone <diego.morone.irb.usi.ch> wrote:
> Dear AMBER users,
>
>
>
> I am trying to set up replica exchange on AMBER. Using explicit solvent
> (ff14SB + TIP3P water) and 16 geometrically spaced replicas I get a good
> range of accept ratios (from 5 to 16 %) and 10-20 round trips/replica, but
> weird histograms (see attachment) which don't look like gaussians. The
> simulation is run for 40ns/replica on 2 GPUs with pmemd.cuda.MPI on Amber
> 19. After heating at 300K, the equilibration was performed first NPT at
> 300K
> 1atm, then NVT at 300K. I get a similar plot with implicit solvent and less
> replicas. Could you help me in spotting the problem?
>
>
>
> Many thanks
>
> Diego
>
>
>
> TREMD
>
> &cntrl
>
> imin = 0,
>
> irest = 0,
>
> ntx = 1,
>
> ntt = 3,
>
> gamma_ln = 1.0,
>
> temp0 = TEMPERATURE,
>
> cut = 9.0,
>
> ntc = 2,
>
> ntf = 2,
>
> nstlim = 10,
>
> dt = 0.002,
>
> ig = RANDOMNUM,
>
> numexchg = 2000000,
>
> iwrap = 1,
>
> ntpr = 5000,
>
> ntwr = 5000,
>
> /
>
> &wt TYPE='END'
>
> /
>
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>
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Received on Wed Aug 05 2020 - 06:00:05 PDT
