Hi Andrew,
> Thanks for your response. The junk in my input file is evolutionary
> leftovers from previous runs. I used a small system and a small cutoff
> because I'm trying to hone in on the problem. I have done several
> dozens
> of picoseconds of qmmm with this system, gradually ramping up from 0K
> to
> 16K at constant pressure. So I don't think that the evolutionary
> leftovers in the input file are causing the problem.
>
> I want to draw your attention to the following:
>
> According to the attached output file (and the qm_region.pdb file), the
> min and max Z are -5.884 and 5.884, which gives a size of 11.76. So
> the z
> size + 2*cutoff is 19.76Ang. But then later in the same output file,
> it
> says the QM Z size is 29.962Ang. Isn't this a conflict? The system
> only
> moved one step. I set it up this way to hone in on the problem.
Ok, I get what you are referring to now. Can you send me your prmtop and
inpcrd file so I can try this. The inpcrd file was not on the original
email. My guess with regards to what may be happening is that you are
starting with a very low initial temperature and also a very low initial
density. This results in the pressure calculation being very inaccurate.
Looking at your output file:
NSTEP = 1 TIME(PS) = 135.063 TEMP(K) = 14.30 PRESS =
6.6
Etot = -14478.3795 EKtot = 54.5737 EPtot =
-14532.9532
BOND = 18.5150 ANGLE = 18.7428 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
-534.9888
EELEC = -4.5737 EHBOND = 0.0000 RESTRAINT =
0.0000
DFTBESCF= -14030.6485
EKCMT = 10.1798 VIRIAL = 8.5837 VOLUME =
11166.4943
Density =
0.6107
Ewald error estimate: 0.6399E+02
The pressure is initially positive so I suspect your box is jumping in size.
This may mean that while the atoms do not move between steps your box size
may be changing considerably. I would be interested to know if this problem
occurs if you run initially with ntb=1.
All the best
Ross
/\
\/
|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
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Received on Tue Apr 20 2010 - 16:00:02 PDT
