Dear AMBER users,
I'm currently starting to work with Accelerated molecular dynamics, and I
am having a weird line in the amd.out.
My amd.in file is the one found in the aMD tutorial (
http://ambermd.org/tutorials/advanced/tutorial22/) modified in the
ethreshd, alphad, alphad and alphad to mach my system:
vt-continue
&cntrl
imin=0,irest=1,ntx=5,
nstlim=50000000,dt=0.002,
ntc=2,ntf=2,ig=-1,
cut=10.0, ntb=1, ntp=0,
ntpr=1000, ntwx=1000,
ntt=3, gamma_ln=2.0,
temp0=300.0,ioutfm=1,iwrap=1,
iamd=3,
ethreshd=2218.9428, alphad=120.4,
ethreshp=−26992.9436, alphap=199860.5,
/
When I run the calculation I instantly get this message in the terminal:
Bad data for namelist object ethreshp
But the calculation carries on and upon inspection of the amd.out I find a
weird line:
Note: ig = -1. Setting random seed to 420367 based on wallclock time in
microseconds.
| Using Accelerated MD (AMD) RASING VALLEYS to enhance sampling iamd = 3
| AMD boost to total energy: EthreshP,alphaP 0.000000000000
199860.500000000000
| AMD boost to dihedrals: EthreshD,alphaD 2218.942800000000
120.400000000000
From where I deduce that ethreshp value is not being read.
Can anyone give me some insight on what can be happening?
Thank you very much,
Claire
claire.coderchboue.ceu.es
Faculty of Pharmacy
Universidad CEU San Pablo
Madrid
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Received on Fri Oct 23 2015 - 10:00:04 PDT
