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:
&cntrl
imin=0,
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,
ntf=2,ntc=2,
nstlim=100000, dt=0.001,
ntwe=100, ntwx=100, ntpr=100, ntwr=-50000,
ntr=0,
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.M
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
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Received on Thu Jul 15 2010 - 02:00:02 PDT
