在 2017/8/20 0:02, David A Case 写道:
> On Sat, Aug 19, 2017, Jiyuan Liu wrote:
>> I could not find note 2 on p.25 from Amber2017 reference.
> The note is there (e.g. at ambermd.org/doc12/Amber17.pdf), and it explains
> how mpi4py is handled. Check the output of the "./configure -mpi ...." step
> for clues about what might have happened.
I have reinstalled AMBER16, and accepted to install minniconda as the
same as the first time installation. The MMPBSA.py.MPI could be
performed in parallel at this time. I thought the only difference
between these two times installation was the configure of mpich2 v3.1.4,
in the first time the configure parameter was "./confifgure
--prefix=/usr/local/mpich2 CFLAGS=-fPIC --enable-shared FC=ifort
CC=icc", and the second time parameter was "./configure CC=icc CXX=icpc
FC=ifort F77=ifort CFLAGS="-fPIC" CXXFLAGS="-fPIC" FFLAGS="-fPIC"
--enable-shared --prefix=/usr/local/mpich2". Would ask you whether the
configure parameter of mpich2 could cause the parallel of MMPBSA.py.MPI
abnormal?
>> Actually, I really like AMBER12, because it is very stable to perform
>> MMPBSA.py.MPI.
> Please report any regressions, or new problems with MMPBSA.py.MPI that you
> find in AmberTools17 vs. earlier versions. Note that MMPBSA is in AmberTools,
> and has nothing to do with cuda (as far as I can tell). The only program
> in Amber12 that involves cuda is pmemd. So it's still hard to see what
> benefit you would get by trying to compile Amber12 with cuda.
I found a new problem with MMPBSA.py.MPI, when I prepare to perform it,
I must type a command "source $AMBERHOME/amber16.sh before. However I
have added the environment parameter in the .bashrc. Another difference
is the ptraj, I could not perform ptraj in amber16, such as the script like:
-----------------------------------------------------------
trajin prod1.mdcrd 1 500 1
trajin prod2.mdcrd 1 500 1
trajin prod3.mdcrd 1 500 1
trajin prod4.mdcrd 1 500 1
trajin prod5.mdcrd 1 500 1
trajin prod6.mdcrd 1 500 1
trajin prod7.mdcrd 1 500 1
trajin prod8.mdcrd 1 500 1
trajin prod9.mdcrd 1 500 1
trajin prod10.mdcrd 1 500 1
cluster out testcluster representative pdb \
average pdb averagelinkage clusters 5 rms @CA
-----------------------------------------------------------
Would ask you how to perform the script above, I tried to perform it
used cpptraj, the error displayed in the follow:
----------------------------------------------------------------------------------------------------------------------
CPPTRAJ: Trajectory Analysis. V17.00
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 08/20/17 22:31:55
| Available memory: 65.847 GB
Reading 'mcl-puma.prmtop' as Amber Topology
Radius Set: modified Bondi radii (mbondi)
INPUT: Reading input from 'cluster.ptraj'
[trajin prod1.mdcrd 1 500 1]
Reading 'prod1.mdcrd' as Amber Trajectory
[trajin prod2.mdcrd 1 500 1]
Reading 'prod2.mdcrd' as Amber Trajectory
[trajin prod3.mdcrd 1 500 1]
Reading 'prod3.mdcrd' as Amber Trajectory
[trajin prod4.mdcrd 1 500 1]
Reading 'prod4.mdcrd' as Amber Trajectory
[trajin prod5.mdcrd 1 500 1]
Reading 'prod5.mdcrd' as Amber Trajectory
[trajin prod6.mdcrd 1 500 1]
Reading 'prod6.mdcrd' as Amber Trajectory
[trajin prod7.mdcrd 1 500 1]
Reading 'prod7.mdcrd' as Amber Trajectory
[trajin prod8.mdcrd 1 500 1]
Reading 'prod8.mdcrd' as Amber Trajectory
[trajin prod9.mdcrd 1 500 1]
Reading 'prod9.mdcrd' as Amber Trajectory
[trajin prod10.mdcrd 1 500 1]
Reading 'prod10.mdcrd' as Amber Trajectory
[cluster out testcluster representative pdb average pdb
averagelinkage clusters 5 rms @CA]
Warning: No clustering algorithm specified; defaulting to 'hieragglo'
CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD
(mask [.CA]) best-fit
Hierarchical Agglomerative: 5 clusters, average-linkage.
Sieved frames will not be included in final cluster distance
calculation.
Cluster # vs time will be written to testcluster
Pairwise distance data set is 'representative[PWD]'
Representative frames will be chosen by lowest cumulative distance
to all other frames.
Warning: Set 'representative' contains no data.
Warning: File 'testcluster' has no sets containing data.
TIME: Total execution time: 0.1176 seconds.
------------------------------------------------------------------------------------------------------------------
Would you guide me how to perform the cluster script using cpptraj or
any other analysis tools. Many thanks.
Kindest regards
Jiyuan
> ....dac
>
>
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Received on Sun Aug 20 2017 - 08:00:02 PDT
