Hi, David
Thank you very much for your suggestions, I am gonna try them.
Best,
Nubia S. Prates
PhD student, Bioinformatics
Universidade Federal de Minas Gerais
________________________________
De: David Case <david.case.rutgers.edu>
Enviado: segunda-feira, 2 de setembro de 2019 13:02
Para: AMBER Mailing List <amber.ambermd.org>
Assunto: Re: [AMBER] issue during TI minimisation
On Mon, Sep 02, 2019, Núbia Prates wrote:
>
>During my TI calculations, I found weird symbols in the parameter DV/DL,
>SC_VDW_DER, and SC_DERIV in my output file from minimization, which only
>happed for lambda = 1.0.
>
>| TI region 1
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 4.1102E+07 8.2342E+04 8.3886E+06 OH 1665
>
> BOND = 317.3157 ANGLE = 904.6059 DIHED = 1310.1921
> VDWAALS = 41162100.8488 EEL = -68177.7272 HBOND = 0.0000
> 1-4 VDW = 370.0347 1-4 EEL = 5174.0882 RESTRAINT = 0.0000
> DV/DL = **************
> Softcore part of the system: 14 atoms, TEMP(K) = 0.00
> SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 114.1430
> SC_BOND= 2.2068 SC_ANGLE= 6.6700 SC_DIHED = 20.1347
> SC_14NB= 5.5231 SC_14EEL= 56.7652 SC_VDW = -0.3269
> SC_EEL = 23.1702
> SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
> SC_EEL_DER= 0.0000 SC_VDW_DER= *********** SC_DERIV = ***********
> ------------------------------------------------------------------------------
Programs compiled with Fortran will put "****" in fields where the
output is too large to fit. Since your starting structure has a very
bad close contacts (look at the VDWAALS energy term), what you describe
is probably something to be expected. Try continuing the minimization:
as the total energy decreases, the values of DV/DL (etc) will probably
get smaller as well, and fit into the output format.
You may, however, need to get a better starting structure: minimization
generally, but not always, can succeed in resolving bad initial
contacts.
....dac
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Received on Tue Sep 03 2019 - 03:30:02 PDT
