Hi,
I am equilibrating my system raising the temperature from 0 to 300K - I want
to start by also equilibrating the pressure doing my simulation in NVT
enzemble so I set my variables using constraits on my protein backbone (10
kcal/mol)
ntx = 1,
ntb = 1,
cut = 12.0,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 10000, dt = 0.001
when I look at my results in VMD the only thing that has really changed is
the box which is no longer square but a strange form. Furthermore if I plot
volume and pressure from the output file the volume is increasing and the
pressure is at 0 - do I need to specify some other parameters for the NVT? I
have also looked at the starting position from the prmtop and rst file and
they look fine. The gradient from the minimization was 10¯2. I use the rst
file from the minimization as -ref for the constraints but that should not
give any problems I would pressume.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 11 2010 - 01:30:04 PDT
