I think I figured out why. The .mdcrd file was from a 10 ns simulation that has yet to complete. I saw that my octagonal box had become twice as big and spherical after > 1 ns. The density was about 1.0, there was no vacuum bubble, so I think it was ok. That was when I posed the question earlier because I wanted to know if it was normal for the octagonal water box to expand even during a PME MD.
I had another complete 10 ns PME NPT on a different protein that worked with cpptraj autoimage.
The outputs are entirely from pmemd.cuda.MPI. Here is the ncdump. Please let me know if there is anything wrong. Thank you in advance.
server2:reduce_ttqy_amber user$ ncdump -h reduce_ttqy_wat_md3.mdcrd
netcdf reduce_ttqy_wat_md3 {
dimensions:
frame = UNLIMITED ; // (0 currently)
spatial = 3 ;
atom = 38847 ;
label = 5 ;
cell_spatial = 3 ;
cell_angular = 3 ;
variables:
char spatial(spatial) ;
float time(frame) ;
time:units = "picosecond" ;
float coordinates(frame, atom, spatial) ;
coordinates:units = "angstrom" ;
char cell_spatial(cell_spatial) ;
char cell_angular(cell_angular, label) ;
double cell_lengths(frame, cell_spatial) ;
cell_lengths:units = "angstrom" ;
double cell_angles(frame, cell_angular) ;
cell_angles:units = "degree" ;
// global attributes:
:title = "default_name" ;
:application = "AMBER" ;
:program = "pmemd" ;
:programVersion = "11.0" ;
:Conventions = "AMBER" ;
:ConventionVersion = "1.0" ;
}
On 2 Aug, 2013, at 11:07 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Fri, Aug 2, 2013 at 8:54 AM, Wang Chern Hoe (Dr) <WangCH.ntu.edu.sg> wrote:
>> [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.
>
> This error indicates there is something strange about the box
> coordinates in your NetCDF trajectory. Is this trajectory directly
> from sander or pmemd MD, or has it been processed in some way already?
> What is the output of 'ncdump -h reduce_ttqy_wat_md3.mdcrd'? You can
> find the 'ncdump' program in your $AMBERHOME/bin directory.
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
CONFIDENTIALITY:This email is intended solely for the person(s) named and may be confidential and/or privileged.If you are not the intended recipient,please delete it,notify us and do not copy,use,or disclose its content.
Towards A Sustainable Earth:Print Only When Necessary.Thank you.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 02 2013 - 09:00:02 PDT
