Here is the output from imin=0:
| # of SOLUTE degrees of freedom (RNDFP): 9309.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 9309. NUM_NOSHAKE = 0 CORRECTED RNDFP = 9309.
| TOTAL # of degrees of freedom (RNDF) = 9309.
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 303.90 PRESS = 0.0
Etot = 36631.3487 EKtot = 2810.9097 EPtot = 33820.4390
BOND = 6250.5412 ANGLE = 1038.1511 DIHED = 1809.7446
1-4 NB = 991.0854 1-4 EEL = 8601.9149 VDWAALS = 32226.2784
EELEC = -14572.2582 EGB = -2525.0184 RESTRAINT = 0.0000
-Aaron
________________________________________
From: Brian Radak [radak004.umn.edu]
Sent: Tuesday, August 06, 2013 5:06 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Trajectory post-processing
Can you post the non-matching output with imin=0 (I assume using nstlim =
0)?
Also the thermostat specifications will be ignored in your input. ntt,
tempi, etc. are unnecessary.
Brian
On Tue, Aug 6, 2013 at 4:50 PM, VanDyne_Aaron <VanDyne_Aaron.roberts.edu>wrote:
> I am looking to use amber to calculate the energies of different
> configurations of a protein-protein interaction. I am trying to use the
> imin=5 option of sander with maxcyc=1, but I am having an issue. The
> outputted energies always have a van der Waals contribution that is on the
> order of 10^16. I am just running a trajectory that has multiple copies of
> the crystal structure as a test. Also, the electrostatics calculated do not
> match those found by using imin=0 and the prmcrd file even though the
> coordinates in my trajectory are the same as those in the prmcrd file. My
> input file is:
>
> Energy calculations
> &cntrl
> imin=5, ntb = 0, maxcyc=1,
> igb = 2, ntpr = 100, ntwx = 100,
> ntt = 3, gamma_ln = 1.0,
> tempi = 300.0, temp0 = 300.0,
> nstlim = 0, dt = 0.001,
> cut = 50.0
> &end
> END
> END
>
> On the command line I enter,
>
> sander -O -i energy.in -o energy.out -p BarnaseBarstar.prmtop -c
> BarnaseBarstar.prmcrd -y BarnaseBarstar.mdcrd
>
> Here is a snapshot of the problematic lines in the output file:
>
> Maximum number of minimization cycles reached.
>
>
> minimizing coord set # 1
>
>
> Maximum number of minimization cycles reached.
>
>
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 1.6770E+16 2.1754E+16 1.3901E+18 O 2379
>
> BOND = 11945445.8414 ANGLE = 430296.1667 DIHED =
> 9376.9433
> VDWAALS = ************* EEL = -11230.6376 EGB =
> -10173.4925
> 1-4 VDW = 8619599.3277 1-4 EEL = 3580.9229 RESTRAINT =
> 0.0000
> minimization completed, ENE= 0.16770484E+17 RMS= 0.217544E+17
>
> What is it that I am doing wrong? Is something wrong with the imin=5
> option of sander?
>
> Thank you,
> -Aaron van Dyne
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Tue Aug 06 2013 - 15:30:02 PDT
