*Thanks Brian.
I ran the minimization only by steepest descent and used the value of
ncyc=500.
But after that while running the equilibration, I am getting the following
error.
I ran the equilibration with and without restrain but I am getting the same
error.*
*** Process received signal ***
Signal: Segmentation fault (11)
Signal code: Address not mapped (1)
Failing at address: 0x2085ed584
[ 0] /lib64/libpthread.so.0 [0x31ff20de80]
[ 1] /usr/local/amber11/exe/sander.MPI(__nblist__grid_ucell+0x18d)
[0x51fbcd]
[ 2] /usr/local/amber11/exe/sander.MPI(__nblist__nonbond_list+0x7d2)
[0x5270f2]
[ 3] /usr/local/amber11/exe/sander.MPI(force_+0x15fc) [0x67914c]
[ 4] /usr/local/amber11/exe/sander.MPI(runmd_+0x2a22) [0x4e31c2]
[ 5] /usr/local/amber11/exe/sander.MPI(sander_+0x5213) [0x4ad453]
[ 6] /usr/local/amber11/exe/sander.MPI(MAIN__+0xe27) [0x4a81c3]
[ 7] /usr/local/amber11/exe/sander.MPI(main+0xe) [0x88da1e]
[ 8] /lib64/libc.so.6(__libc_start_main+0xf4) [0x31fe61d8b4]
[ 9] /usr/local/amber11/exe/sander.MPI [0x43a799]
*** End of error message ***
*The out file after equilibration is given below:*
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
| # of SOLUTE degrees of freedom (RNDFP): 226379.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 226376. NUM_NOSHAKE = 0 CORRECTED RNDFP = 226376.
| TOTAL # of degrees of freedom (RNDF) = 226376.
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 490840
| TOTAL SIZE OF NONBOND LIST = 8527410
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 10.53 PRESS =
0.0
Etot = ************** EKtot = 2367.4279 EPtot =
**************
BOND = 1393.1235 ANGLE = 10557.5817 DIHED =
78749.4150
1-4 NB = 1961.7190 1-4 EEL = 113643.6928 VDWAALS =
9116.2567
EELEC = ************** EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.9193E-08
------------------------------------------------------------------------------
Regards
Vipul Garg
On Wed, Feb 8, 2012 at 7:24 PM, Brian Radak <radak004.umn.edu> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > 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.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Debostuti Ghosh Dastidar
PhD Scholar
Computational Biophysics Lab
Department of Biotechnology
Indian Institute of Technology Madras
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Received on Thu Feb 09 2012 - 03:00:02 PST
