AMBER Archive (2003)

Subject: Re: AMBER: FEP problem

From: David A. Case (case_at_scripps.edu)
Date: Thu Sep 18 2003 - 10:08:18 CDT

On Thu, Sep 18, 2003, Itziar Maestre Asenjo wrote:

> The FEP simulation runs OK and I have no error message in the output
> file, but I found that in the lasts windows of the simulation the value
> of the z-coordinate for my molecule is infinite, thus I cannot see my
> molecule grafically with any program (I have no restart file, and the
> trajectory file is not complete)
>
> Here is the input file I am using:
>
> Calcul FEP de 200 finestres de 100ps
> Temperatura constant 300k
> &cntrl
> ntx=5, ntb=0,
> ntt=1, temp0=300.0,
> nstlim=-1,
> ntc=2, scee=1.2,
> ntpr=100000, ntwx=100000,
    ^^^^^^^^^^^^^^^^^^^^^^^^

You need to set the above variables to much smaller values. If you only
print something and save the trajectory every 100,000 steps, you have no
hope of monitoring whether or not the simulation was actually proceeding
correctly or not. If you are having problems, you need to monitor the
results every 100 steps or so.

..good luck...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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