[AMBER] vlimit exceeding situtaion with ntt option

From: Vijay Manickam Achari <vjrajamany.yahoo.com>
Date: Thu, 15 Jul 2010 08:30:20 +0000 (GMT)

Dear Amber experts,

Here I would like to post a question about 'vlimit exceeded' situtaion.
I am simulating membrane system.
The md-production-script.in is as blow in amber10:

   irest=1, ntx=5,
   scnb=1.0, scee=1.0,
   iwrap = 1,
   ntt=3, gamma_ln = 1.0,
   temp0=348.0, tautp=0.2,
   ntb = 2, ntp=1, taup=0.2,
   nstlim=100000, dt=0.001,
   ntwe=100, ntwx=100, ntpr=100, ntwr=-50000,
   cut = 9.0

If I used this script to run the simulation, the simulation terminates saying the vlimit exceeded.

If I delete ( ntt=3, gamma_ln = 5.0) and replace with ntt=2, the simulation runs without terminating.

Here is my doubt. What is the significant difference between ntt=3 and ntt=2 ? I understand that it is heating the system with different protocol.
By the way, is my simulation valid in the case of using ntt=2, especially for membrane system in explicit water?

Thanks in advance for any guidance.


Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,


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Received on Thu Jul 15 2010 - 02:00:02 PDT
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