AMBER Archive (2009)

Subject: [AMBER] REMD fixed atoms

From: Maxime Louet (maxime.louet_at_etudiant.univ-rennes1.fr)
Date: Fri Jan 30 2009 - 11:26:08 CST

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


rms_replica1.jpg
rms_replica16.jpg

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