On Fri, Oct 08, 2010, William Flak wrote:
> In other words, I created a group of atoms connected together, I want to
> keep this of atoms together, regardless the interaction between them.
There's no way to do this outside of modifying the code.
> I used ntr=1 option with defining the restrain parameters. But, during
> minimization, the job stops after 800 step without any error.
Are you running a parallel job? If so, maybe the error showed up in one of
the other outputs...
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 750 -5.5923E+03 4.0307E-01 5.1912E+00 ZA 1
>
> BOND = 369.4249 ANGLE = 0.5592 DIHED = 0.0000
> VDWAALS = 909.1502 EEL = -6872.0083 HBOND = 0.0000
> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.5675
> EAMBER = -5592.8739
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 800 -2.7801E+04 1.1340E+05 4.7350E+06 O 197
>
> BOND = 594.3819 ANGLE = 8.6889 DIHED = 0.0000
> VDWAALS = 1254.2891 EEL = -29686.0122 HBOND = 0.0000
> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 27.3736
> EAMBER = -27828.6522
Looks like you are getting two atoms on top of each other. Run an 800-step
minimization, and look at the structure at the end. If you have waters,
remember that there are no Lennard-Jones parameters on HW, and you have to use
SHAKE to prevent things like this happening. I gather you have made some of
your own force field parameters (since you have an atom named "ZA"); if so,
make sure that you can't allow opposite charges to come too close together.
....dac
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Received on Sat Oct 09 2010 - 06:00:03 PDT
