AMBER Archive (2009)

Subject: Re: [AMBER] Etot positive

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Nov 16 2009 - 05:13:55 CST

it's not possible to say since we don't know what you are simulating. if
this were a solute in water I would say there is probably something wrong.

On Mon, Nov 16, 2009 at 12:06 AM, Jio M <jiomm_at_yahoo.com> wrote:

> Dear Amber users;
>
>
>
> 1) Is it necessary that Etot should be negative .... I have seen in
> most of the querries and tutorial output, that Etot is negative.
>
> I used the following input for equilibrium phase after heating from 0 -
> 300K
>
> here is equilibrium input:
>
> &cntrl
>
> imin = 0, irest = 1, ntx = 7,
>
> ntb = 2, pres0 = 1.0, ntp = 1,
>
> taup = 2.0,
>
> cut = 10.0, ntr = 0,
>
> ntc = 2, ntf = 2,
>
> tempi = 300.0, temp0 = 300.0,
>
> ntt = 3, gamma_ln = 1.0,
>
> nstlim = 100000, dt = 0.002,
>
> ntpr = 100, ntwx = 100, ntwr = 1000
>
>
>
> these last steps energy output values
>
>
>
> NSTEP = 99900 TIME(PS)
> = 249.800 TEMP(K) =
> 295.30 PRESS = -56.5
>
> Etot = 6133.5908
> EKtot = 3811.4443
> EPtot =
> 2322.1465
>
> BOND =
> 635.3000 ANGLE =
> 1956.2672 DIHED
> = 405.6718
>
> 1-4 NB = 195.6267 1-4
> EEL = 4000.9903
> VDWAALS = -4121.3236
>
> EELEC = -750.3858
> EHBOND =
> 0.0000 RESTRAINT
> = 0.0000
>
> EKCMT = 673.1555
> VIRIAL = 788.8184
> VOLUME = 94811.4804
>
>
> Density
> = 1.2381
>
> Ewald error estimate: 0.5658E-03
>
>
> ------------------------------------------------------------------------------
>
>
>
>
>
> NSTEP = 100000 TIME(PS)
> = 250.000 TEMP(K) =
> 299.31 PRESS = 59.6
>
> Etot = 6178.0066
> EKtot = 3863.0849
> EPtot =
> 2314.9217
>
> BOND =
> 674.1848 ANGLE =
> 1878.4011 DIHED
> = 425.5195
>
> 1-4 NB = 189.5570 1-4
> EEL = 4010.5437
> VDWAALS = -4097.2245
>
> EELEC = -766.0599
> EHBOND =
> 0.0000 RESTRAINT
> = 0.0000
>
> EKCMT = 685.0976
> VIRIAL = 563.0999
> VOLUME = 94823.4042
>
>
> Density
> = 1.2380
>
> Ewald error estimate: 0.1530E-03
>
>
>
>
>
> Is there anything wrong in starting structures or input files??
>
>
>
> please suggest
>
>
>
>
>
> thanks and regards;
>
> Jiomm
>
>
>
>
>
>
>
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