Here is the input file I tried:
&cntrl
ntwx = 100,
ntwe = 100, ntwr = 50, ntpr = 1000, ntxo = 1, ioutfm = 1,
imin = 0,
ntx = 1,
temp0 = 300,
tempi = 300,
ig = -1,
nstlim = 20000,
dt = 0.002,
ntb = 0,
nscm = 100,
ntc = 2, ntf = 2,
ntt = 3, vrand = 1000,
gamma_ln = 10.0,
igb = 1, cut = 9999.0,
ntpr = 1,
nmropt = 1,
ntr = 1,
restraintmask = ':1-X_LASTREC_RESIDNO_X & !.H= ',restraint_wt = 5,
/
&wt type='END', /
DISANG=./restraints.in
where restraints.in file looks like:
&rst
iat=1620,1625,
ialtd=1, r1= 0, r2= 0.1, r3= 15, r4= 15.1,
rk2=5, rk3=5,
/
Prior to running this production step, I ran five steps of minimization:
minimization 01 - implicit solvent
&cntrl
imin = 1, maxcyc = 1000, ncyc = 100,
ntx = 1, ntc = 1, ntf = 1,
ntb = 0, ntp = 0, ntxo = 1, ioutfm = 1,
ntwx = 100, ntwe = 0, ntpr = 100,
igb = 1, cut = 999.0,
ntr=1,
restraintmask = ':1-X_LASTREC_RESIDNO_X & !.H= | :X_LIG_RESIDNO_X.CG',
restraint_wt=2.0,
&end
END
minimization 02
&cntrl
imin = 1, maxcyc = 1000, ncyc = 100,
ntx = 1, ntc = 1, ntf = 1,
ntb = 0, ntp = 0, ntxo = 1, ioutfm = 1,
ntwx = 100, ntwe = 0, ntpr = 100,
igb = 1, cut = 999.0,
ntr = 1, restraintmask = ':1-X_LASTREC_RESIDNO_X & !.H= |
:X_LIG_RESIDNO_X.CG', restraint_wt=1.0,
&end
END
minimization 03
&cntrl
imin = 1, maxcyc = 1000, ncyc = 100,
ntx = 1, ntc = 1, ntf = 1,
ntb = 0, ntp = 0, ntxo = 1, ioutfm = 1,
ntwx = 100, ntwe = 0, ntpr = 100,
igb = 1, cut = 999.0,
ntr = 1, restraintmask = ':1-X_LASTREC_RESIDNO_X & !.H= |
:X_LIG_RESIDNO_X.CG', restraint_wt=0.1,
&end
END
minimization 04
&cntrl
imin = 1, maxcyc = 1000, ncyc = 100,
ntx = 1, ntc = 1, ntf = 1,
ntb = 0, ntp = 0, ntxo = 1, ioutfm = 1,
ntwx = 100, ntwe = 0, ntpr = 100,
igb = 1, cut = 999.0,
ntr = 1, restraintmask = ':1-X_LASTREC_RESIDNO_X & !.H= |
:X_LIG_RESIDNO_X.CG', restraint_wt=0.05,
&end
END
minimization
&cntrl
imin = 1, maxcyc = 1000, ncyc = 100,
ntx = 1, ntc = 1, ntf = 1,
ntb = 0, ntp = 0, ntxo = 1, ioutfm = 1,
ntwx = 100, ntwe = 0, ntpr = 100,
igb = 1, cut = 999.0,
/
However, it still shows the message about coordinate overflow as before.
The five minimization steps run fine. The error occurs in the 06md.in
script (stage).
Let me know what you think I should try next.
On Fri, Nov 4, 2022 at 10:40 AM David A Case <david.case.rutgers.edu> wrote:
> On Thu, Nov 03, 2022, Prithviraj Nandigrami via AMBER wrote:
>
> >
> >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.
>
> Something is going wrong with your simulation. Try setting ntt=3,
> gamma_ln=10.0 ... that might help. But run a short simulation with ntpr=1,
> so you (and we) will know how many steps into the simulation the error
> occurreed. Look carefully at the mdout file for any signs of problems.
>
> ....dac
>
>
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Received on Fri Nov 04 2022 - 16:30:03 PDT
