AMBER Archive (2009)

Subject: Re: [AMBER] REMD fixed atoms

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sun Feb 01 2009 - 12:00:33 CST

is your amber fully patched? also try without repcrd.
look at the output files- are the temperatures what you requested?

On Fri, Jan 30, 2009 at 12:26 PM, Maxime Louet <
maxime.louet_at_etudiant.univ-rennes1.fr> wrote:

> Dear all,
>
> I am a new user of Amber 9 and I'm trying to simulate a small peptide
> dimers using REMD, FF96, igb=5 and no restraint.
> However, I have some problems. The calculations works fine (without any
> error message), but when I analyse the trajectory of any single replica, it
> seems that the backbones and lateral chains doesn't move (even at high
> temperature), see attached files for the RMSD of replica 1 and 16.
> Using the same kind of input with regular sander (no REMD) lead to totally
> "normal" simulation. Does anybody have an answer ?
>
> I used 16 replicas with 32 processors, temperatures are between 190K and
> 503K.
> Here is one of my input for the replica starting with T=190 :
> &cntrl
> imin=0, irest=1, ntx=5,
> nstlim=1000, dt=0.002,
> ntc=2, ntf=2,
> ntt=3, gamma_ln=50,
> tempi=0.0, temp0=190.0,
> ntpr=500, ntwx=500,
> ntb=0, igb=5,
> gbsa=1, saltcon=0.15,
> cut=25.0, rgbmax=25.0,
> repcrd=1, numexchg=12500,
> /
>
> Thank you in advance, for the time you will spend to answer my question.
>
> Maxime Louet
>
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