Re: [AMBER] weird energy histograms with REMD

From: Diego Morone <diego.morone.irb.usi.ch>
Date: Wed, 5 Aug 2020 14:53:44 +0200

Hi Koushik,

Thanks for your reply. Colors are indeed different temperatures. I extracted
the potential energies from the mdouts and the replica indices with cpptraj,
then sorted the energies with the numpy.take function

-----Original Message-----
From: koushik kasavajhala <koushik.sbiiit.gmail.com>
Sent: mercoledý, 5 agosto 2020 14:43
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] weird energy histograms with REMD

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 - 06:00:06 PDT
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