Dear Amber Users,
I ran MD simulation for 10 ns and then tried to run aMD with following
parameters
---------------------------------------------------------
Accelerated MD - explicit solvent
&cntrl
imin=0, irest=0, ntx=1, nstlim=25000000, dt=0.002, iwrap=1,
ntb=2, cut=10.0, ntp=1, ntc=2, ntf=2, tempi=300.0, temp0=300.0,
ioutfm=1, ntt=3, gamma_ln=1.0, ig=-1, iamd=1,
EthreshP=-152417, alphaP=13330, barostat=2, ntpr=5000, ntwr=5000,
ntwx=5000
&end
-------------------------------------------------------------------------
I encountered with this error while running aMD. My normal MD simulation
run to get parameters also ran with pmemd.cuda which ran fine. Here is the
final output file for that.
A V E R A G E S O V E R 1000 S T E P S
NSTEP = 5000000 TIME(PS) = 10100.0 TEMP(K) = 299.95 PRESS
= -1.5
Etot = -302570.25 EKtot = 73158.56 EPtot =
-375728.8244
BOND = 2365.12 ANGLE = 6165.20 DIHED = 9862.4871
1-4 NB = 2781.82 1-4 EEL = 21490.98 VDWAALS = 43693.4265
EELEC = -462087.88 EHBOND = 0.00 RESTRAINT = 0.0000
EKCMT = 32326.40 VIRIAL = 32365.48 VOLUME = 1192465.2387
Density = 1.0238
------------------------------------------------------------------------------
Visual inspection of the pdb structure generated from rst file also looks
normal.
Although, I am not sure why aMD output file shows higher temperature at the
first step
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = *437.64*
PRESS = 0.0
Etot = -58253.34 EKtot = 106742.86 EPtot =
-164996.20
BOND = 2353.15 ANGLE = 6119.93 DIHED =
9847.52
1-4 NB = 2754.62 1-4 EEL = 21776.16 VDWAALS =
43983.47
EELEC = -462590.85 EHBOND = 0.00 RESTRAINT = 0.00
EAMD_BOOST = 210759.76
EKCMT = 0.0000 VIRIAL = 0.00 VOLUME = 1192520.97
Density = 1.0238
-----------------------------------------------------------------
Could any one suggest possible solution?
Many thanks,
Ash
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Received on Fri Apr 20 2018 - 15:00:02 PDT
