Hi all,
I need to run a simulation of a protein fragment with a bound ligand in
explicit water using pmemd.cuda. To keep things from falling apart, I'd
lke to restrain all boundary residues that used to be connecting the
fragment to the rest of the protein. Here, there are some complications
with different versions of pmemd giving different outcomes.
First, pmemd and pmemd.cuda don't seem to accept restraintmask keyword
(sander works fine), and only read residue groups specified after the
parameter list.
The initial minimization runs fine, with the entire protein restrained
(pmemd.cuda works).
The problems begin when multiple residue sets are restrained at the
second stage of minimization (protein is relaxed along with the
solvent). The full set of residues to be restrained is in the format below:
Set 1
1000.0
RES 1
END
Set 2
1000.0
RES 24 43
END
...
END
There is a total of 12 residue groups.
Here's the command line: /data/amber11/exe/pmemd.cuda -O -i wat_min2.in
-o complex_wat_min2.out -p complex_wat.prmtop -c complex_wat_min1.rst -r
complex_wat_min2.rst -x complex_wat_min2.mdcrd -ref complex_wat_min1.rst
pmemd.cuda fails. When I work my way backwards by removing residue
groups, I get alternating segmentation faults and "unspecified launch
failure launching kernel kNLClearCellBoundaries" errors. Finally, at
only the first 3 residue groups it starts working and finishes the
minimization. Not sure how to explain that.
The cpu version (pmemd) runs this minimization with full input with no
incident (mpirun on 8 cores). sander works as well.
Are there some unfinished issues with pmemd.cuda that affect restraints
handling?
When I get the result from the partially restrained protein minimization
(all 12 groups with pmemd), I'm trying to run heating. At this point, I
use the same set of constraints and this command line:
/data/amber11/exe/pmemd.cuda -O -i wat_heat.in -o complex_wat_heat.out
-p complex_wat.prmtop -c complex_wat_min2.rst -r complex_wat_heat.rst -x
complex_wat_heat.mdcrd -ref complex_wat_min2.rst
pmemd.cuda generates a segmentation fault, while CPU version of pmemd
says "PMEMD terminated abnormally!" and leaves this message in the
output file:
Coordinate resetting cannot be accomplished,
deviation is too large
iter_cnt, my_bond_idx, i and j are: 1 444 869 870
sander gives a similar complaint citing SHAKE not being able to run.
When I look at the restart files, the system seems to behave as expected
- the restrained residues are all in place after two rounds of
minimization, and the others have moved.
Is there anything I can do here to get this to work? Is there a limit on
the number of restrained groups hard-coded somewhere? Is there a deeper
problem in this case? I can send the full input files and/or prmtop/rst
files, if needed.
Any suggestions would be greatly appreciated
Thank you
Sasha
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Received on Tue Aug 24 2010 - 17:30:03 PDT
