I recommend you to check Amber manual for NTB in.
NTB = 2 means pressure control.
Or to learn Amber tutorial for DNA simulation well.
IK
-----Original Message-----
From: Vaibhav Dixit [mailto:vaibs1.gmail.com]
Sent: Monday, April 22, 2013 4:47 PM
To: amber.ambermd.org
Subject: [AMBER] Fwd: Input file for NVT simulation
Hello,
I am new to MD simulations using AMBER. I want to know what should be the
paramteres in input files for running a NVT simulation in AMBER.
Is this ok?
polyA-polyT 10-mer: 100ps MD
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2,
cut = 10.0, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 50000, dt = 0.002,
ntpr = 100, ntwx = 100, ntwr = 1000
/
This lead to the pressure being zero everytime in simulation. Is it
accepted? Or should I put give any values to NTP, pres0 ?
thanks in advance!
--
*Vaibhav Dixit
*
*Undergraduate Student*
*Chemical Science and Technology*
*Indian Institute of Technology Guwahati,India*
*
*
*Alt Email: v.dixit.iitg.ac.in*
--
*Vaibhav Dixit
*
*Undergraduate Student*
*Chemical Science and Technology*
*Indian Institute of Technology Guwahati,India*
*
*
*Alt Email: v.dixit.iitg.ac.in*
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Received on Mon Apr 22 2013 - 01:30:06 PDT
