RE: AMBER: MD simulation error

From: Ross Walker <>
Date: Tue, 24 Jul 2007 18:01:13 -0700

Hi Lili,
Most probably it is to do with time step - you are suing a 5fs time step and
while you fix all bonds (ntf=3, ntc=3) this is still likely too large - take
a look at your trajectory file and see what it looks like. Note I don't
think ntf>2 is used much so you may want to check that it actually works
properly for your system - is there a reason why you want to keep all the
bonds fixed? You should note that most things have not been parameterized to
run in this mode so I would be very cautious of your results - make sure you
can prove that your choice to keep the bonds fixed is justified - I.e.
perhaps try this out on some model systems and show that you can recover the
same results for the entity you are interested in whether you fix all bonds
or just bonds to hydrogen.
You also have an extremely large gamma_ln value.
All the best

|\oss Walker

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From: [] On Behalf Of
Lili Peng
Sent: Tuesday, July 24, 2007 16:54
Subject: AMBER: MD simulation error

Dear all,

I am getting the following error for my MD simulation:

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 1 7 16 28
     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.

My input file is the following:

310K constant temp MD
  imin=0, ntb=1,
  cut=8.0, ntc=3, ntf=3,
  tempi=310.0, temp0=310.0,
  ntt=3, gamma_ln=50,
  nstlim=10000, dt= 0.005,
  ntpr=1, ntwx=1,

Does anyone have any idea why this occurs? Does it have anything to do with
the timestep?

Thank you for your time,

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Received on Wed Jul 25 2007 - 06:07:43 PDT
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