Hi;
Yes, this worked. Thanks!
-Sergio
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Monday, February 07, 2011 6:12 PM
To: AMBER Mailing List
Subject: Re: [AMBER] XMIN ERROR in LMOD calculation
Hi,
One issue with LMOD that sometimes pops up is atomic overlap of atoms
with zero VDW parameters (e.g. HO, HW, ho) during local minimization.
If your topology file is named prmtop.in you can run the program
'lmodprmtop prmtop.in prmtop.out' to get a topology file (prmtop.out)
which creates small VDW barriers for these atoms to prevent overlap.
Try this, run the calc with the modified topology file and see if the
problem still occurs. See the end of the LMOD section in the manual
for some more details on this.
-Dan
On Mon, Feb 7, 2011 at 7:34 PM, Wong, Sergio E. <wong105.llnl.gov> wrote:
> Hi;
>
> I am lmod calculations on a parallel version of sander (Amber 10). Unfortunately, some of my calculations stop with the following error message:
>
> XMIN ERROR -4
>
> Sometimes this happens even after several iterations of the LMOD algorithm i.e.
>
> ...
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 26 -9.7501E+03 9.8869E-01 3.8575E+01 H22 6477
>
> BOND = 289.5861 ANGLE = 1198.0072 DIHED = 4060.6548
> VDWAALS = -3408.4998 EEL = -29544.6812 EGB = -4708.5113
> 1-4 VDW = 1387.7714 1-4 EEL = 20689.8016 RESTRAINT = 285.8172
> EAMBER = -10035.8712
>
> End of LMOD requested XMIN relaxation
> Start of LMOD requested XMIN relaxation
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 1.0771E+04 9.8869E-01 6.5058E+03 O 4154
>
> BOND = 15604.5419 ANGLE = 2083.9978 DIHED = 4111.8390
> VDWAALS = 274.3960 EEL = -30206.3812 EGB = -4325.4192
> 1-4 VDW = 1873.4051 1-4 EEL = 20728.9000 RESTRAINT = 626.0818
> EAMBER = 10145.2793
>
>
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 33 -1.0885E+07 1.4863E+10 1.2723E+12 O 930
>
> BOND = 1748.6644 ANGLE = 1996.5821 DIHED = 4120.1470
> VDWAALS = -3096.9955 EEL = ************* EGB = -4578.5845
> 1-4 VDW = 1431.2920 1-4 EEL = 20713.6816 RESTRAINT = 343.3575
> EAMBER = *************
>
> End of LMOD requested XMIN relaxation
> Start of LMOD requested XMIN minimization
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -1.0885E+07 1.4863E+10 1.2723E+12 O 930
>
> BOND = 1748.6644 ANGLE = 1996.5821 DIHED = 4120.1470
> VDWAALS = -3096.9955 EEL = ************* EGB = -4578.5845
> 1-4 VDW = 1431.2920 1-4 EEL = 20713.6816 RESTRAINT = 343.3575
> EAMBER = *************
> XMIN ERROR: Status is -4
>
>
>
> The input for one of the runs follows:
>
> &cntrl
> imin = 1,
> ntx =1,
> maxcyc = 2000,
> ncyc = 2100,
> ntb = 0,
> ntmin=4,
> ntpr=1,
> ntr=1,
> ntrx=1,
> igb = 5,
> cut = 15,
> ntr=1,
> restraint_wt=100,
> restraintmask=':413 > .6.0 '
> /
> &lmod
> conflib_size = 30,
> number_lmod_iterations = 30,
> total_low_modes = 10,
> explored_low_modes = 5,
>
> number_free_rotrans_modes = 0,
> energy_window = 50.0,
> lmod_minimize_grms = 0.1,
>
> arnoldi_dimension = 50,
> matrix_vector_product_method = 'forward',
> frequency_eigenvector_recalc = 6,
>
> lmod_restart_frequency = 5,
> restart_pool_size = 3,
>
> number_lmod_moves = 0,
> lmod_step_size_max = 5.0,
> lmod_step_size_min = 2.0,
> lmod_relax_grms = 1.0,
>
> Monte_Carlo_method = 'Metropolis',
> rtemperature = 1.5,
>
> number_ligands = 1,
> ligstart_list = '[6449]',
> ligend_list = '[6502]',
> ligcent_list = '[0]',
> rotmin_list = '[20]',
> rotmax_list = '[180]',
> trmin_list = '[0.1]',
> trmax_list = '[1.0]',
>
> frequency_ligand_rotrans = 1,
> number_ligand_rotrans = 5,
>
> conflib_filename = '701339-1.lmod_dock_conflib',
> lmod_trajectory_filename = '701339-1.lmod_dock_trajectory',
> lmod_job_title = '701339-1 lmod-dock test job',
>
> lmod_verbosity = 2,
>
> random_seed = 314159,
>
> lbfgs_memory_depth = 3,
> xmin_method = 'LBFGS',
> xmin_verbosity = 0
> /
>
> Does anyone have any suggestions?
>
> Thanks;
>
> -Sergio
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>
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Received on Tue Feb 08 2011 - 18:00:03 PST
