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From: Stregone <stregone.protonmail.com>

Date: Thu, 04 Aug 2016 05:08:37 -0400

Dear Daniel,

You have made a good point. The answer to your question, quote

"Is my final energy lower than my initial energy?" - Yes , it is.

NSTEP ENERGY RMS GMAX NAME NUMBER

1 1.3253E+05 3.3470E+01 1.0140E+02 C4 14764

NSTEP ENERGY RMS GMAX NAME NUMBER

80000 1.9963E+04 9.5323E-03 4.1860E-01 H7 20803

But this is only the minimisation. Now I am more confident about the minimisation results,

but what really is concerning me is the energies from the system equilibration "NPT",

For example, so far now

NSTEP = 389800 TIME(PS) = 494.900 TEMP(K) = 296.50 PRESS = 18.8

Etot = 63496.2933 EKtot = 22986.4857 EPtot = 40509.8076

BOND = 5076.8827 ANGLE = 51676.7748 DIHED = 9130.7612

1-4 NB = 1780.3492 1-4 EEL = -2172.1523 VDWAALS = -20696.7763

EELEC = -4286.0317 EHBOND = 0.0000 RESTRAINT = 0.0000

EKCMT = 2260.4126 VIRIAL = 2092.0633 VOLUME = 414092.6196

Density = 1.5847

Ewald error estimate: 0.1640E-02

------------------------------------------------------------------------------

A college said that during the system equilibration, the resulting energies should have

negative sign. But, since the minimisation, the energy is positive.

if the I assume that for the equilibration the "zero point" is the energy from the minimisation,

then the results seem to make sense, as the system heat, then after some time it finds

a equilibrium.

But, if in fact the energy should have negative sign, then all is wrong.

I would say that it is a bit tricky to deal with this issue.

-------- Original Message --------

Subject: Re: [AMBER] AmberÂ´14 Solvent box simulation, something went wrong!!

Local Time: August 3, 2016 7:30 PM

UTC Time: August 3, 2016 7:30 PM

From: daniel.r.roe.gmail.com

To: amber.ambermd.org

Hi,

The absolute value of the energies you get for a system don't really

tell you much, since the zero point is not well-defined. What is more

important is the relative energy between different conformations. So

in your case, the real question is "Is my final energy lower than my

initial energy?". If the answer is "yes", then the minimization ran

just fine (although whether you have run enough minimization is a

different question). If the answer is "no" then you may have a

problem...

-Dan

On Wed, Aug 3, 2016 at 7:43 AM, Stregone <stregone.protonmail.com> wrote:

*> 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.
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

Date: Thu, 04 Aug 2016 05:08:37 -0400

Dear Daniel,

You have made a good point. The answer to your question, quote

"Is my final energy lower than my initial energy?" - Yes , it is.

NSTEP ENERGY RMS GMAX NAME NUMBER

1 1.3253E+05 3.3470E+01 1.0140E+02 C4 14764

NSTEP ENERGY RMS GMAX NAME NUMBER

80000 1.9963E+04 9.5323E-03 4.1860E-01 H7 20803

But this is only the minimisation. Now I am more confident about the minimisation results,

but what really is concerning me is the energies from the system equilibration "NPT",

For example, so far now

NSTEP = 389800 TIME(PS) = 494.900 TEMP(K) = 296.50 PRESS = 18.8

Etot = 63496.2933 EKtot = 22986.4857 EPtot = 40509.8076

BOND = 5076.8827 ANGLE = 51676.7748 DIHED = 9130.7612

1-4 NB = 1780.3492 1-4 EEL = -2172.1523 VDWAALS = -20696.7763

EELEC = -4286.0317 EHBOND = 0.0000 RESTRAINT = 0.0000

EKCMT = 2260.4126 VIRIAL = 2092.0633 VOLUME = 414092.6196

Density = 1.5847

Ewald error estimate: 0.1640E-02

------------------------------------------------------------------------------

A college said that during the system equilibration, the resulting energies should have

negative sign. But, since the minimisation, the energy is positive.

if the I assume that for the equilibration the "zero point" is the energy from the minimisation,

then the results seem to make sense, as the system heat, then after some time it finds

a equilibrium.

But, if in fact the energy should have negative sign, then all is wrong.

I would say that it is a bit tricky to deal with this issue.

-------- Original Message --------

Subject: Re: [AMBER] AmberÂ´14 Solvent box simulation, something went wrong!!

Local Time: August 3, 2016 7:30 PM

UTC Time: August 3, 2016 7:30 PM

From: daniel.r.roe.gmail.com

To: amber.ambermd.org

Hi,

The absolute value of the energies you get for a system don't really

tell you much, since the zero point is not well-defined. What is more

important is the relative energy between different conformations. So

in your case, the real question is "Is my final energy lower than my

initial energy?". If the answer is "yes", then the minimization ran

just fine (although whether you have run enough minimization is a

different question). If the answer is "no" then you may have a

problem...

-Dan

On Wed, Aug 3, 2016 at 7:43 AM, Stregone <stregone.protonmail.com> wrote:

-- ------------------------- Daniel R. Roe, PhD Department of Medicinal Chemistry University of Utah 30 South 2000 East, Room 307 Salt Lake City, UT 84112-5820 http://home.chpc.utah.edu/~cheatham/ (801) 587-9652 (801) 585-6208 (Fax) _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Aug 04 2016 - 02:30:02 PDT

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