Dear David,
I was able to apply cpptraj autoimage for the 1 ns PME NPT trajectory.
However, when I tried to apply cpptraj autoimage for the next 10 ns PME NPT trajectory, this is what I got:
CPPTRAJ: Trajectory Analysis. V13.12
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
INPUT: Reading Input from STDIN
[parm reduce_ttqy_wat.prmtop]
AmberParm Title: [default_name]
Radius Set: modified Bondi radii (mbondi)
[trajin reduce_ttqy_wat_md3.mdcrd]
NETCDF Error: NetCDF: Index exceeds dimension bound
Error: Getting cell lengths.
Error: Could not set up reduce_ttqy_wat_md3.mdcrd for reading.
Error: trajin: Could not set up trajectory.
On 2 Aug, 2013, at 8:26 PM, David A Case <case.biomaps.rutgers.edu> wrote:
> On Fri, Aug 02, 2013, Wang Chern Hoe (Dr) wrote:
>>
>> I did a 10 ns explicit water (octagonal box) PME NPT simulation after
>> a 20 ps PME NVE equilibration. I noticed the water molecules expanding
>> beyond the initial octagonal box, and remaining as spherical droplet of
>> water with the protein molecule in the centre. The volume remains more
>> or less constant. Is this normal ?
>
> Sounds like you need to re-image your molecules into a central unit cell.
> See the "autoimage" command in cpptraj (or, if you just have a single protein
> surrounded by water, the "image" command in ptraj.)
>
> ...dac
>
>
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Received on Fri Aug 02 2013 - 08:00:03 PDT
