Hello,
On Wed, Sep 29, 2010 at 12:48 PM, nicholus bhattacharjee <
nicholusbhattacharjee.gmail.com> wrote:
> Dear community,
> I am running some constant pH MD simulation at pH
> 1,3,5,9. For pH 1,3,9 i could do the simulation upto 3 nano seconds. But
> for
> pH 5
> after 319 pico seconds following error is given in output file
>
>
>
> NSTEP = 159500 TIME(PS) = 319.000 TEMP(K) = 300.11 PRESS =
> 0.0
> Etot = -1622.9227 EKtot = 1500.7689 EPtot =
> -3123.6915
> BOND = 402.1849 ANGLE = 1163.1859 DIHED = 1317.5274
> 1-4 NB = 434.2169 1-4 EEL = 6405.9433 VDWAALS = -727.6820
> EELEC = -10167.4300 EGB = -1951.6380 RESTRAINT =
> 0.0000
> -----------------------------
> -------------------------------------------------
>
> vlimit exceeded for step 159643; vmax = 82.4458
>
This right here hints at your problem. It looks like a couple of atoms have
come very close to one another, or some other source of large forces caused
one atom to go flying away too rapidly. You should visualize your
trajectory to see if you can see what's happening. The resulting clash is
causing SHAKE to fail, which is causing the simulation to bomb out.
See if you can reproduce the problem at the same step (maybe you need to
minimize and heat to relax bad contacts).
Good luck!
Jason
Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 0 15 1 4
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
>
> I am not understanding the problem. Is restarting will help. Please help.
> Thank you in advance.
>
>
> --
> Nicholus Bhattacharjee
> PhD Scholar
> Department of Chemistry
> University of Delhi
> Delhi-110007 (INDIA)
> Phone: 9873098743(M)
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Sep 29 2010 - 10:00:20 PDT
