AMBER: QM/MM NPT Simulation

From: Daniel Oehme <>
Date: Fri, 20 Apr 2007 14:46:14 +1000

Dear Amber Community,

I am currently trying to do some QM/MM simulations on a drug (DG35; 73
atoms) in a 10A box of methanol using AMBER9. I have minimized the
system, heated it to 300K then equilibrated using PMEMD. Following
this I ran a short QM/MM equilibration before wanting to run a QM/MM
production phase. However, I am unable to do this as I cannot get the
system to equilibrate. Here is my input file for the QM/MM

300K constant temp QMMMMD - 250ps Equilibration
  imin=0, irest = 1, ntx = 5,
  ntb=2, pres0 = 1.0,
  ntp=1, taup=2.0,
  ntc=2, ntf=2, cut=6.0,
  ntt=1, tempi=300.0, temp0=300.0,
  nstlim=250000, dt=0.001,
  ntpr=100, ntwx=2500, ifqnt=1
  qm_ewald=1, qm_pme=1

I find that I am getting a consistently positive pressure which means
that the volume increases and consequently, the density decreases to
non-natural values for methanol (0.4). It is at this stage that
sander.QMMM crashes due to "volume of ucell too big, too many

I have continued the PMEMD simulation into the production phase so I
dont think the problem has to do with the drug-methanol system. I have
also tested the QM/MM equilibration with ntt=3 but got the same

Can anyone give me any advice on what I should try next or any
literature I should read?

Daniel Oehme
PhD Student
La Trobe University
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Received on Sun Apr 22 2007 - 06:07:38 PDT
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