Re: [AMBER] weird energy histograms with REMD

From: koushik kasavajhala <koushik.sbiiit.gmail.com>
Date: Wed, 5 Aug 2020 18:13:03 +0530

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
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