AMBER Archive (2007)

Subject: Re: Fwd: Re: AMBER: Minimization amber9 segmentation fault

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Mon Dec 03 2007 - 16:18:01 CST

OK even maxcyc=500 in total time 339 (100% all processors).

A question about present status of the system.

Judging from

NSTEP ENERGY RMS GMAX NAME NUMBER
      1 4.4840E+09 2.4571E+08 8.2511E+10 C216 9120

 BOND = 149932.4186 ANGLE = 46211.6820 DIHED = 9161.8416
 VDWAALS = ************* EEL = -246175.6118 HBOND = 0.0000
 1-4 VDW = 29126.1421 1-4 EEL = 23905.1720 RESTRAINT = 0.0000

to

NSTEP ENERGY RMS GMAX NAME NUMBER
    500 -2.8141E+05 7.0948E-01 1.8222E+02 C29 4048

 BOND = 17679.7273 ANGLE = 1747.5980 DIHED = 7313.4743
 VDWAALS = 28428.8493 EEL = -363382.6658 HBOND = 0.0000
 1-4 VDW = 2703.4773 1-4 EEL = 24034.2277 RESTRAINT = 66.8632
 EAMBER = -281475.3119
]
(actually 520 steps because I used rst). Which values of ENERGY and GMAX should
be reached with (as in present case) protein-ligand restrained 30.0 before
relaxing the latter? Also, should this minimization be completed with conjugate
gradient, or is this one only to make the process faster?

Thanks
francesco

--- Francesco Pietra <chiendarret_at_yahoo.com> wrote:

> Great! With
>
> 1st minimization protein_ligand_pop_box80x80
> &cntrl
> imin=1, maxcyc=20, ntmin=2,
> cut=10, ntb=1, ntpr=1,
> ntr=1, restraintmask=":77-520, 521",
> restraint_wt=30,
> /
>
> it completed the (small) task (third attempt, in parallel). It should not be
> forgot that I had removed some severe clashes before the third attempt: the
> first attempt would have probably killed even steepest descent (not tried,
> though I could try on demand for maxcyc=20, ncyc=10). Now I'll try
> maxcyc=500,
> otherwise as in the successful run.
>
> Thanks a lot
>
> francesco
>
>
>
> --- "David A. Case" <case_at_scripps.edu> wrote:
>
> > On Mon, Dec 03, 2007, Francesco Pietra wrote:
> >
> > > I removed all WAT residues at a distance <=1.5A from POPC residues from
> the
> > > membrane already bearing a cavity. Then inserted the protein-complex and
> > > built the TIP3P box with leap. Then run the minimization again. Starting
> > > energy was 9 orders of magnitude less that previous run (which had
> crashed
> > > because WAT 534 had clashes with POP 24) and gradient and energy
> decreased
> > > by only 2 orders of magnitude. Again segmentation fault.
> >
> > Segmentation faults can be very difficult to diagnose, since there can be
> > many
> > causes. Ordinarily, sander would not segfault on minimization just because
> > of bad overlaps.
> >
> > What I would do:
> >
> > 1. Try a serial minimzation to see if there is some weird parallelization
> > problem. You are only trying to do a short minimization, so you should
> > reduce
> > your exposure to other problems.
> >
> > 2. Only do steepest descent minimization with a bad structure. Conjugate
> > gradient minimization (which by defaults starts after 10 steps,) can take
> > very
> > large trial steps, which might somehow be violating implicit assumptions
> > about
> > periodicity that leads to memory corruption (just guessing here, but
> avoiding
> > conjugate gradients until you have a better structure is definitely a good
> > idea.)
> >
> > 3. If that fails, you will probably have to remove the initial bad
> contacts
> > and see if that helps.
> >
> > ...dac
> >
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>
>
>
>
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