Re: [AMBER] number of frames read in

From: Jason Swails <>
Date: Wed, 23 Mar 2011 11:55:04 -0700


I can see how it would be confusing, but Dwight's email is correct. That is
the startframe and endframe for every mdcrd file. If you want to be able to
specify just those frames, you'll have to use ptraj to combine all of the
trajectories and use that trajectory with

One further comment. I strongly suggest that you use NetCDF format files
when running MD. will process NetCDF trajectories automatically,
and there are many advantages to using NetCDF over ASCII trajectories.
(higher precision coordinates, far more compressed, no fixed-width
coordinate fields so coordinate values won't be replaced by *****,
independent frames so that 1 corrupted frame doesn't ruin the trajectory,
and it processes orders of magnitude faster than ASCII trajectories for
every program that processes them including sander, ptraj, and VMD, and
writes much faster so it will improve pmemd's performance noticeably).

To create NetCDF trajectories in sander or pmemd, just add the variable
"ioutfm=1" to the &cntrl namelist.

Hope this helps,

On Wed, Mar 23, 2011 at 9:44 AM, Chris Chris <> wrote:

> Please help me understand my issue here. I have run two simulations in
> series,
> the first for 5ns and the second for 5 ns. The second 5ns simulation is
> merely a
> continuation of the first. My file for the production simulation
> is as
> follows:
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=2500000,dt=0.002,
> ntc=2,ntf=2,
> cut=8.0, ntb=2, ntp=1, taup=2.0,
> ntpr=500, ntwx=500,
> ntt=3, gamma_ln=2.0,
> temp0=300.0,
> /
> thus, I am generatring a frame per ps, correct? If so, the 2 simulations
> must
> comprise 10,000 frames- is this assumption correct?
> I am interested in reading frames 6,000-8,000 into and thus
> obtain
> binding data. I have the submit file for as follows:
> mpirun -np 4 /gpfs1/apps/chemistry/amber/amber11/bin/ -O -i
> -o G1TETRA_RESULTS_MMPBSA.dat -sp -cp
> -rp g1tetra_dimer1_no
> -lp -y g1tetra_prod_mdx*
> My thinking is that the program will read in both trajectories and choose
> frames
> 6,000-8,000 and process them. However, this does not work as I get the
> following
> error message:
> FYI ptrajSetupIO(): trajin stop value (8000) is greater than the number of
> sets
> read in.
> Setting stop to the maximum value (5000)
> WARNING in ptrajSetupIO(): trajectory start is > stop; no
> configurations will be processed
> Thus, only 5,000 frames are read. However- 10,000 should be present.
> Can anyone help me with this?
> Thanks
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Wed Mar 23 2011 - 12:00:04 PDT
Custom Search