Thank you for the helpful suggestions. I am doing tests by reducing the
force constant values.
I also encountered another error for some of the MD frames:
Error: '*' encountered (atom 6 X). This indicates coordinate overflow.
Error: '*' encountered (atom 6 Y). This indicates coordinate overflow.
Error: '*' encountered (atom 6 Z). This indicates coordinate overflow.
Error: '*' encountered (atom 7 X). This indicates coordinate overflow.
.........
Can you please tell me what this error could potentially stem from? Here is
the MD input file:
&cntrl
ntwx = 100,
ntwe = 100, ntwr = 50, ntpr = 1000, ntxo = 1, ioutfm = 0,
imin = 0,
ntx = 1,
temp0 = 300,
tempi = 300,
ig = -1,
nstlim = 20000,
dt = 0.002,
ntb = 0,
nscm = 100,
ntc = 2, ntf = 2,
ntt = 2, vrand = 1000,
igb = 1, cut = 999.0,
iwrap = 1
nmropt = 1,
ntr = 1,
restraintmask = ':1-X_LASTREC_RESIDNO_X & !.H= ',restraint_wt = 100,
/
&wt type='END', /
DISANG=./restraints.in
My restraints.in file looks like:
&rst
iat=1620,1625,
ialtd=1, r1= 0, r2= 0.1, r3= 15, r4= 15.1,
rk2=1.5, rk3=1.5,
/
Thank you.
On Wed, Nov 2, 2022 at 10:15 PM Thomas Cheatham <tec3.utah.edu> wrote:
>
> > I was wondering if there is a section in the amber manual that deals with
> > the amber20 GPU input file set up specifically? Also, this error seems to
> > be popping up intermittently - not easy to reproduce.
>
> No there is not. For the fast GPU implementations, a mixed fixed precision
> / single precision model is the default and this means there is a limited
> range in values for forces that do not blow the number format. If you run
> double precision, it will be more tolerant or run on the CPUs where it is
> double precision and more forgiving of numerical blow up (yet maybe not of
> large force constants that can effect integration time step, etc). In
> general, large force constants for restraints should be avoided since this
> leads to a large range of numerical values (that blow up the precision
> model). What we would question is why do you need a large force constant?
> If you think of positional restraints with an Angstrom-kcal**2, even small
> deviations lead to large numbers. Big deviations will make the integrator
> fail, SHAKE fail, etc. I do not recall the original e-mail, but think of
> very small force constants for restraints, otherwise dial back the
> integration time step to much smaller.
>
> That is my advise (ing).
>
> > > >| WARNING :: The NMR distance restraint between atoms 9524 and 4574
> could
> > > >| be stretched to an unsafe degree. The run will proceed,
> but
> > > >| overflow in the force accumulation is possible.
>
> p.s. good that we have that warning - pre-emptive - reduce force
> constants or time step or both.
>
> --tec3
>
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Received on Thu Nov 03 2022 - 15:00:02 PDT
