Hi, David,
Thanks for your advice, i tried to change the tempi as well as the ntt value
as you suggested, however, both no luck, i still got the same error message,
and as I wrote in another email, i noticed that the bond energy from the
last step of minimization decreased dramatically when I started to run the
equilibration.
Here is the output of the last step of the minimization:
---------------------------------------------------------------------------------------------------------------
NSTEP ENERGY RMS GMAX NAME NUMBER
5000 -2.0193E+05 5.2652E-01 7.9133E+01 FE 12110
BOND = 13557.7748 ANGLE = 2100.0258 DIHED =
6683.4797
VDWAALS = 24316.5978 EEL = -284589.3077 HBOND =
0.0000
1-4 VDW = 2495.1800 1-4 EEL = 33508.5993 RESTRAINT =
0.0000
------------------------------------------------------------------------------------------------------------------
and here is the output of the equilibration of the system with restraints on
the solute:
-------------------------------------------------------------------------------------------------------------------
| Local SIZE OF NONBOND LIST = 17919959
| TOTAL SIZE OF NONBOND LIST = 17919959
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = -215088.9939 EKtot = 0.0000 EPtot = -
215088.9939
BOND = 396.4313 ANGLE = 2100.0258 DIHED =
6683.4797
1-4 NB = 2495.1800 1-4 EEL = 33508.5993 VDWAALS =
24316.5978
EELEC = -284589.3078 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.1110E-03
vlimit exceeded for step 0 ; vmax = Infinity
Coordinate resetting (SHAKE) was not accomplished
within 3000 iterations
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
---------------------------------------------------------------------------------------------------------------------
As can be seen, the bond energy changed from 13557.7748 to 396.4313 while
all other energies remained the same, is this happening because I changed
the ntc, ntf value from the minimization to the md?
Can anyone suggest how to solve this problem please?
Thanks in advance!
Rachel
On 11/8/06, David A. Case <case.scripps.edu> wrote:
>
> On Wed, Nov 08, 2006, Rachel wrote:
>
> > vlimit exceeded for step 0 ; vmax = Infinity
> >
> > tempi = 0.0,
> > temp0 = 300.0,
> > ntt = 3,
> > gamma_ln = 1.0,
>
> As a wild guess, try a short (10 step) simulation with tempi set to some
> small
> but non-zero value. It is possible that Langevin dynamics has some bad
> behavior when all the velocities are zero. Alternatively, try a short
> simulation with ntt=1.
>
> This is shooting in the dark, but it is simple enough to be worth a try.
>
> ...good luck....dac
>
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Received on Sun Nov 12 2006 - 06:07:10 PST
