[AMBER] Amber´14 Solvent box simulation, something went wrong!!

From: Stregone <stregone.protonmail.com>
Date: Wed, 03 Aug 2016 09:43:18 -0400

Good morning Amber users!!

I am running a minimisation of a org. solvent box (bromobenzene),
the box is 40x40x40, a small one.
After the minimisation and the equilibrium, the energies (ETOT, EPTOT and EKTOT ),
are positive, which should not be possible. I do not think that the problem is on the minimisation,
so I assume that it should be on the NPT script.

This is the script for the minimisation
-----------------------------------------------------------------------------------------------------------------------
minimisation
&cntrl
imin = 1, maxcyc = 80000, ntmin = 1,
ntx = 1,
ncyc = 25000,
ntb = 1, ntp = 0,
cut = 12.0
/
----------------
The last part of the output is something like this
--------------->>>>
NSTEP ENERGY RMS GMAX NAME NUMBER
80000 1.9963E+04 9.5323E-03 4.1860E-01 H7 20803

BOND = 142.2302 ANGLE = 47287.8987 DIHED = 229.8498
VDWAALS = -20567.1982 EEL = -6658.3096 HBOND = 0.0000
1-4 VDW = 1659.8453 1-4 EEL = -2131.1922 RESTRAINT = 0.0000
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Build the list 5.06 ( 8.70% of List )
| Other 53.09 (91.30% of List )
| List time 58.15 ( 1.55% of Nonbo)
| Short_ene time 1839.59 (91.87% of Direc)
| Other 162.84 ( 8.13% of Direc)
| Direct Ewald time 2002.44 (54.17% of Ewald)
| Adjust Ewald time 26.17 ( 0.71% of Ewald)
| Self Ewald time 0.25 ( 0.01% of Ewald)
| Fill Bspline coeffs 49.43 ( 8.46% of Recip)
| Fill charge grid 39.85 ( 6.82% of Recip)
| Scalar sum 79.28 (13.57% of Recip)
| Grad sum 55.30 ( 9.46% of Recip)
| FFT back comm time 67.48 (21.75% of FFT t)
| Other 242.84 (78.25% of FFT t)
| FFT time 310.32 (53.11% of Recip)
| Other 50.16 ( 8.58% of Recip)
| Recip Ewald time 584.34 (15.81% of Ewald)
| Force Adjust 1022.74 (27.66% of Ewald)
| Virial junk 42.43 ( 1.15% of Ewald)
| Start synchronizatio 0.32 ( 0.01% of Ewald)
| Other 18.21 ( 0.49% of Ewald)
| Ewald time 3696.90 (98.45% of Nonbo)
| Nonbond force 3755.26 (89.55% of Force)
| Bond/Angle/Dihedral 82.15 ( 1.96% of Force)
| FRC Collect time 201.65 ( 4.81% of Force)
| Other 154.20 ( 3.68% of Force)
| Force time 4193.25 (100.0% of Runmd)
| Runmd Time 4193.25 (93.41% of Total)
| Other 295.86 ( 6.59% of Total)
| Total time 4489.15 (100.0% of ALL )
-----------------------------------------------------------------------------------------------------------------------
The NPT is the following :
>>NPT - Bromobenzene
>>&cntrl
>>imin = 0,
>>irest = 0, ntx = 1, ntc = 2,
>>ntb = 2, cut = 13.0,
ntp = 1, taup = 1.0, pres0 = 1.013,
tempi = 298.15, temp0 = 298.15,
ntt = 3, gamma_ln = 3.0, ig = -1,
nstlim = 600000, dt = 0.0005,
ntpr = 200, ntwx = 200, ntwr = 200, ntwe = 200,
/
&ewald
skinnb = 2.0
/
-----------------------------------------------------------------------------------------------------------------------------
I read big part of the manual, -Sander- so most of the commands come from there and
the suggestions into it.
I started a new simulation few minutes ago, so I am attaching the NPT so far !!
As you can see, the energies are positive.

I would appreciate any advise. Thanks before hand.

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Received on Wed Aug 03 2016 - 07:00:03 PDT
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