This functionality is controlled by:
*ifmbar* If set to 1 (Default = 0), additional output is generated for
later postprocessing.
*mbar_states* number of lambda windows considered.
* mbar_lambda *lambda windows simulated.
For example, if you want to run mbar with 15 lambda windows at 0.00, 0.05,
0.10, 0.15, 0.20, 0.30, 0.40, 0.50, 0.60, 0.70, 0.80, 0.85, 0.90, 0.95,
1.00, you would use the following options:
ifmbar = 1, mbar_states = 15, mbar_lambda = 0.00, 0.05, 0.10, 0.15, 0.20,
0.30, 0.40, 0.50, 0.60, 0.70, 0.80, 0.85, 0.90, 0.95, 1.00,
The options below have been deprecated. They are here for anyone using
AMBER 16 or older, but will not work in AMBER 18.
*bar_intervall *Compute potential energies every bar_intervall steps
(Default = 100)
*bar_l_min *Minimum λ-value (Default = 0.1)
*bar_l_max *Maximum λ-value (Default = 0.9)
*bar_l_incr *The increment to increase λ by between the minimum and maximum
(Default = 0.1)
*from amber18 manual page 430.*
Good luck
On Tue, Sep 24, 2019 at 3:35 AM HOCHEOL LIM <ihcdatabank.gmail.com> wrote:
> Dear All,
>
> I am trying to simulate thermodynamic integration tutorials with pmemd.cuda
> (GPU) implemented in Amber18.
>
> In tutorials (A9),
> there are three steps (discharge, vdw-bonded, recharge).
>
> In vdw-bonded step, I got error messages.
> In discharge or recharge steps, I didn't get error messages.
>
> When I compared to input files in discharge and recharge steps,
> there are only differences in next sentence.
>
> <discharge> or <recharge>
> ifsc=0, crgmask=':1.O1,H6',
>
> <vdw_bonded>
> ifsc=1, scmask1=':1.H6', scmask2=':2.O1,H6', crgmask=':1.H6 | :2.O1,H6'
>
> What value should I set for mbar_states and mbar_lambda ?
>
> The error messages follow.
>
> Note: ig = -1. Setting random seed to 75620 based on wallclock time in
> microseconds.
> | irandom = 1, using AMBER's internal random number generator (default).
> | ERROR: mbar_states not set, please set mbar_states to the number of
> lambdas you wish sample
> | ERROR: mbar_lambda not set, please set mbar_lambda to the lambdas you
> wish to sample
> | ERROR: bar_l_min/max/incr are deprecated. please put all lambdas you
> wish to sample in mbar_lambda and set mbar_states = the total number of
> lambdas
>
> Input errors occurred. Terminating execution.
>
>
> input file (ti.in) follows.
>
> TI simulation
>
> &cntrl
>
> imin = 0, nstlim = 100000, irest = 1, ntx = 5, dt = 0.002,
>
> ntt = 3, temp0 = 300.0, gamma_ln = 2.0, ig = -1,
>
> ntc = 2, ntf = 1,
>
> ntb = 2,
>
> ntp = 1, pres0 = 1.0, taup = 2.0,
>
> ioutfm = 1, iwrap = 1,
>
> ntwe = 1000, ntwx = 10000, ntpr = 10000, ntwr = 20000,
>
>
>
> icfe = 1, clambda = 1.0, scalpha = 0.5, scbeta = 12.0,
>
> logdvdl = 1,
>
> ifmbar = 1, bar_intervall = 1000, bar_l_min = 0.0, bar_l_max = 1.0,
>
> bar_l_incr = 0.1,
>
> timask1 = ':1', timask2 = ':2',
>
> ifsc=1, scmask1=':1.H6', scmask2=':2.O1,H6', crgmask=':1.H6 | :2.O1,H6'
>
> /
>
>
>
> &ewald
>
> /
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Hosein Geraili Daronkola
Ph.D. student,
Wissenschaftspark Potsdam-Golm
Max Planck Institute of Colloids and Interfaces
Theory and Bio-Systems Department
Office K-1.119
Am Mühlenberg 1 OT Golm
14476 Potsdam
Germany
Phone: +49-(0)331 567-9611
Fax: +49-(0)331 567-9602
E-mail: hosein.geraili.mpikg.mpg.de
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Received on Tue Sep 24 2019 - 00:00:02 PDT
