Hello,
You should keep replies to the amber list so others benefit from the
discussion. pmemd will only print trajectories when you are running MD.
This was true for sander as well up until version 10 or 11 (I think it was
11). This was implemented by someone doing extensive QM/MM calculations
that wanted to see how the structures minimized (especially since each step
can take hours if you're using a sufficiently high level QM method with a
large enough QM subsystem).
That functionality has not been ported to pmemd, so what you're seeing is
expected (and documented, I think) behavior.
Hope this helps,
Jason
On Mon, Apr 4, 2011 at 12:19 PM, Indrek Morell <indrekm80.hot.ee> wrote:
> I'm using Amber11, with Bugfix.all applied on 23 January
>
> Actually this is really strange because for some reason PMEMD started
> giving *.mdcdr out when doing MD, but still not when minimizing the system
> (imin=1)... sander gives trajectories in both cases still.
>
> Molecule is short DNA solvated in TIP3PBOX (6)
>
> Command lines are:
>
> ###Min###
>
> mpirun -np 4 ./pmemd.MPI -O -i $AmberRun/Test/Min.prm -o
> $AmberRun/Test/MinMPI.out -p $AmberRun/Test/Test.prmtop -c
> $AmberRun/Test/Test.crd -r $AmberRun/Test/MinMPI.crd -x
> $AmberRun/Test/MinMPI.mdcrd
>
> ###MD###
>
> mpirun -np 4 ./pmemd.MPI -O -i $AmberRun/Test/MD.prm -o
> $AmberRun/Test/MDMPI.out -p $AmberRun/Test/Test.prmtop -c
> $AmberRun/Test/MinMPI.crd -r $AmberRun/Test/MDMPI.crd -x
> $AmberRun/Test/MDMPI.mdcrd
>
> And parameters are:
>
> ###Min.prm###
>
> &cntrl
> cut=8,
> igb=0,
> imin=1,
> maxcyc=100,
> ncyc=20,
> nscm=0, C
> ntb=2,
> ntmin=1;
> ntp=1,
> ntpr=100,
> ntr=0
> ntwx=1,
> /
>
> ###MD.prm###
>
> &cntrl
> cut=8.0,
> dt=0.001,
> gamma_ln=1,
> ig=-1
> igb=0,
> imin=0,
> irest=0,
> isgld=0
> !iwrap=1,
> nscm=0,
> nstlim=1000,
> ntb=2,
> ntc=1,
> ntp=1,
> ntpr=1000,
> ntr=0
> ntt=3,
> ntwr=1000,
> ntwx=10,
> pres0=1,
> taup=1,
> temp0=300,
> tempi=0,
> tempsg=1
> /
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Apr 04 2011 - 12:30:09 PDT
