Hi Vipul,
Based on my personal experience, doing a large number of conjugate gradient
steps can lead to the kinds of stabilities in EEL that you see, although
that in itself is probably not the reason (maybe something with rigid water
being deformed or some spurious interaction with a charge with no LJ
term?).
In those cases, the solution that usually works for me is just to set
"ncyc" and "maxcyc" to the same number so that only steepest descent moves
are made. If you are just trying to remove bad contacts, I can't imagine
getting too different of a result with this approach.
If you are trying to find an actual local minimum, then you probably want
to use a different minimizer anyway (such as xmin).
Regards,
Brian
On Wed, Feb 8, 2012 at 5:18 AM, DEBOSTUTI GHOSHDASTIDAR <
debostutighosh.gmail.com> wrote:
> *Hey,
> I am running energy minimization for my system which has about 73000
> atoms.
> When I am running the minimization for 100 steps the run completes
> successfully
> and out file looks like :
>
> * NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 1.4558E+15 2.3809E+14 5.5356E+16 C5 5835
>
> BOND = 40047.4549 ANGLE = 10141.4764 DIHED =
> 76221.5972
> VDWAALS = ************* EEL = -60118.5281 HBOND =
> 0.0000
> 1-4 VDW = -34.0547 1-4 EEL = 117801.0429 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 50 2.3583E+05 1.2760E+01 8.2187E+01 H1 71988
>
> BOND = 8802.3719 ANGLE = 21825.8477 DIHED =
> 80315.6734
> VDWAALS = 78916.6197 EEL = -72724.4312 HBOND =
> 0.0000
> 1-4 VDW = 2354.3939 1-4 EEL = 116338.6029 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 100 -8.5191E+03 3.0206E+05 8.7596E+07 O65 63415
>
> BOND = 5961.6961 ANGLE = 14103.1166 DIHED =
> 80913.8411
> VDWAALS = -23699.9865 EEL = -199399.8959 HBOND =
> 0.0000
> 1-4 VDW = 2609.4867 1-4 EEL = 110992.6021 RESTRAINT =
> 0.0000*
>
> But when I am running 500 steps the run halts after steepest descent and
> out file
> is given below:*
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 50 2.3583E+05 1.2760E+01 8.2187E+01 H1 71988
>
> BOND = 8802.3719 ANGLE = 21825.8477 DIHED =
> 80315.6734
> VDWAALS = 78916.6197 EEL = -72724.4312 HBOND =
> 0.0000
> 1-4 VDW = 2354.3939 1-4 EEL = 116338.6029 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 100 1.2487E+05 3.2003E+02 8.7537E+04 O 75650
>
> BOND = 2470.7927 ANGLE = 10545.2590 DIHED =
> 78730.8251
> VDWAALS = 8884.1451 EEL = -91339.0075 HBOND =
> 0.0000
> 1-4 VDW = 1959.1686 1-4 EEL = 113621.9506 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 150 -1.1183E+08 3.0136E+11 8.2418E+13 O 75650
>
> BOND = 2469.8463 ANGLE = 10545.1527 DIHED =
> 78730.8067
> VDWAALS = 8883.7540 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 1959.1648 1-4 EEL = 113621.8986 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 200 -3.3519E+07 2.7219E+10 7.4442E+12 H66 55486
>
> BOND = 2469.8462 ANGLE = 10545.1527 DIHED =
> 78730.8067
> VDWAALS = 8883.7540 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 1959.1648 1-4 EEL = 113621.8986 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 250 -7.0670E+07 1.2051E+11 3.2958E+13 H66 55486
>
> BOND = 2469.8462 ANGLE = 10545.1527 DIHED =
> 78730.8067
> VDWAALS = 8883.7540 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 1959.1648 1-4 EEL = 113621.8986 RESTRAINT =
> 0.0000
>
> ... RESTARTED DUE TO LINMIN FAILURE ...
>
>
> *
> Someone please help me out in solving the problem.*
>
> Thanks
> Vipul Garg
> Final year student
> Dept. of Biotechnology
> IIT Madras, Chennai-600036
> INDIA
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>
--
================================ 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 Wed Feb 08 2012 - 06:00:04 PST
