Dear amber friends,
I am trying to simulate a box with two drugs inside, they are the same molecule a figure is attached. I use iwrap in my eq stage , which I understand is the right way to go in multi stage simulations (eq or md production). But I get a warning about only one of the two molecules on the output file, every time a step details are written:
---------------------------------------------------
wrapping first mol.: -42.08192 29.75641 51.53962
NSTEP = 500 TIME(PS) = 201.000 TEMP(K) = 199.17 PRESS = 0.0
Etot = -56056.1447 EKtot = 6849.3528 EPtot = -62905.4975
BOND = 19.7002 ANGLE = 59.8382 DIHED = 136.2303
1-4 NB = 28.4433 1-4 EEL = -192.3433 VDWAALS = 11463.3184
EELEC = -74420.6846 EHBOND = 0.0000 RESTRAINT = 0.0000
Ewald error estimate: 0.2680E-03
------------------------------------------------------------------------------
wrapping first mol.: -42.08192 29.75641 51.53962
wrapping first mol.: -42.08192 29.75641 51.53962
NSTEP = 1000 TIME(PS) = 202.000 TEMP(K) = 203.07 PRESS = 0.0
Etot = -55660.5853 EKtot = 6983.6866 EPtot = -62644.2719
BOND = 16.8732 ANGLE = 62.3180 DIHED = 133.7621
1-4 NB = 33.9226 1-4 EEL = -192.1938 VDWAALS = 11268.7970
EELEC = -73967.7510 EHBOND = 0.0000 RESTRAINT = 0.0000
Ewald error estimate: 0.3213E-03
------------------------------------------------------------------------------
What does it mean? Something is wrong?
Here is the input file, as you can see is the first heating stage of 5.
#
&cntrl
timlim=999999., imin=0,
ntx=1, iwrap=1,
ntxo=1, ntpr=500, ntwx=500, ntwv=0, ntwe=0, ioutfm=1,
ntp=0, ntc=2,
ntb=1, ntf=2, cut=9.0,
ntt=3, temp0=150.0, tempi=100.0, ig=-1, gamma_ln=4.0,
nstlim= 100000, dt=0.002,
A grep shows it even clearer:
eq1.out:wrapping first mol.: -63.12288 0.00000 0.00000
eq1.out:wrapping first mol.: -63.12288 0.00000 0.00000
eq2.out:wrapping first mol.: -42.08192 29.75641 51.53962
eq2.out:wrapping first mol.: -42.08192 29.75641 51.53962
Thasnk!!
FAbian
_______________________________
Fabian Glaser, PhD
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL
fglaser.technion.ac.il
Tel: +972 4 8293701
Fax: +972 4 8225153
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Received on Thu Jan 29 2015 - 01:00:02 PST