[AMBER] wrong estimation of hydrogen velocities when using SHAKE?

From: Jose Borreguero <borreguero.gmail.com>
Date: Tue, 10 Mar 2009 12:09:48 -0400

Dear Amber users,

I am running NPT simulations and apparently the speeds of the hydrogens are
systematically underestimated roughly by a factor of sqrt(2). I have checked
with two different proteins and two different temperatures, having same

I am using the SHAKE algorithm, so I ignore how hydrogen velocities are
estimated in this case.

Below is my input file:

imin=0, irest=1, ntx=5,
ntt=0, tempi=300 ,temp0=300, tautp=1.0,
ntb=1, ntc=2, ntf=2, nsnb=10,
nstlim=250000, dt=0.001,
ntwe=1000, ntpr=1000, ntwx=20, ntwv=20
cut=10.0, ntr=1, nmropt=0,
#Apply restraints to the solute atoms
RES 162 176

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Received on Wed Mar 11 2009 - 01:25:30 PDT
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