Dear Mr. Swails,
Thank you for rapid and useful relpy.
Yours sincerely,
Ikuo KURISAKI
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Monday, October 17, 2011 8:00 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Energy calculateion from MD trajectory: can we skip the
minimization?
A minimization of 1 step is just a single-point energy evaluation, no
minimization is actually done. These are the energies (droids) you're
looking for.
HTH,
Jason
On Mon, Oct 17, 2011 at 2:58 AM, kurisaki <
kurisaki.ncube.human.nagoya-u.ac.jp> wrote:
> Dear Amber developers,
>
>
>
> Thank you for usual kind support.
>
>
>
> I am now trying to calculate energy component by using sander on Amber11.
>
> Energy calculation was done and proper values were obtained.
>
> But I just worry whether obtained energy values were really those derived
> from the input snapshots,
>
> Thus, not the energy derived from minimized structures.
>
>
>
> Amber11 manual says in p26
>
> "If maxcyc=1, then the output file can be
>
> used to extract the energies of each of the coordinate sets in the inptraj
> file."
>
> And I follow that.
>
>
>
> While in my sander output, I found the statements:
>
> "Maximum number of minimization cycles reached."
>
> and the following calculation logs
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
>
> 1 -9.8754E+03 1.2450E+01 6.5958E+01 NH2 1744
>
>
>
> BOND = 0.0000 ANGLE = 2318.2691 DIHED =
> 3019.2679
>
> VDWAALS = -2244.5840 EEL = -22758.6673 EGB =
> -2679.6571
>
> 1-4 VDW = 1075.6518 1-4 EEL = 11320.3164 RESTRAINT =
> 0.0000
>
> ESURF = 74.0312
>
>
>
> Do I need not to worry about these sentences and believe I obtained the
> expected information on energy?
>
> Or I need to set additional parameter (e.g. avoiding MINIMIZATION PROCESS)
> to achieve what I want to know?
>
>
>
> I am most grateful if you give me some advices.
>
>
>
> Yours sincerely,
>
>
>
> Ikuo KURISAKI
>
>
>
> PS
>
>
>
> In my input file, imin, maxcyc and idecomp were set as 5, 1, 2,
> respectively,
>
> And the following mdin file was used.
>
>
>
> #decompose energy on a per-residue basis on the trajectory
>
> &cntrl
>
> imin = 5, igb = 5, gbsa = 2, rgbmax = 8.21,
>
> ntx = 1, maxcyc = 1,
>
> ntc = 2, ntf = 2,
>
> ntb = 0, ntp = 0,
>
> ntwe = 0, ntpr = 500, ntwx=1,
>
> cut = 9, idecomp = 2,
>
> /
>
> Residues considered as REC
>
> RRES 1 295
>
> END
>
> Residues considered as LIG
>
> LRES 296 296
>
> END
>
> Residues to print
>
> RES 1 295
>
> END
>
> END
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Oct 17 2011 - 05:00:03 PDT
