I tried the short run with 10.0 as target temperature and I got
vlimit exceeded for step 0; vmax = **********
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 0 1256 3754 3755
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
Should I repeat the minimization?
On Sat, 19 Sep 2020 at 15:31, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Try setting ntpr and ntwx to 1 in order to get step-by-step energy and
> structure.
>
> Also I'd try a short run with 10.0 target temperature to see if slower
> warming might be possible. I believe using solute restraints during
> warming is normal nowadays, and may be your ultimate solution, but I'd
> also look at the demos for gradual warming cases.
>
> Bill
>
>
> On 9/19/20 2:53 AM, Jisha B wrote:
> > Dear all,
> > I am dealing with a large system of protein-RNA-DNA. I have minimized the
> > system. But when I started the heating stage where I have to increase the
> > temperature from 0K to 100K, it is stuck at
> >
> > 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 = 101843086
> > | TOTAL SIZE OF NONBOND LIST = 101843086
> >
> > NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
> > 0.0
> > Etot = -1363415.9230 EKtot = 0.0000 EPtot =
> > -1363415.9230
> > BOND = 2311.6832 ANGLE = 4410.0196 DIHED =
> > 19869.1201
> > 1-4 NB = 5810.6688 1-4 EEL = 39862.6725 VDWAALS =
> > 207873.5245
> > EELEC = -1643553.6116 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > Ewald error estimate: 0.6217E-04
> >
> > It has been in this stage for last one hour. My input for heating is
> > Heating Equilibration - constant volume
> > &cntrl
> > imin = 0,
> > irest = 0,
> > ntx = 1,
> > ntb = 1,
> > cut = 10.0,
> > ntr = 0,
> > ntc = 2,
> > ntf = 2,
> > tempi = 0.0,
> > temp0 = 100.0,
> > ntt = 3,
> > gamma_ln = 1.0,
> > nstlim = 100000, dt = 0.002
> > ntpr = 100, ntwx = 100, ntwr = 1000
> > /
> > When I repeated the simulation, I got the error vlimt exceeded error. How
> > to solve this?
> >
> --
> Phobrain.com
>
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>
--
Jisha B.
G-Tech Computer Education,
Kerala,
India.
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Received on Sat Sep 19 2020 - 03:30:03 PDT
