Dear AMBER Users,
I have a question about running REMD with AMOEBA.
I tried to run REMD with sander.MPI in AMBER9 at first, but saw the error
message in the mdout file:
"amoeba is not (yet) available in parallel."
Later I tried the same thing with AMBER10. I didn't see the above error
message, but the program always stopped unexpectedly with no error message
when exchanges started (segmentation fault). I searched in the source code a
little bit, and found that the program stopped at the subroutine
remd_exchange (when the program call MPI_allgather). I also did the test on
none AMOEBA remds in AMBERHOME/ test/rem_wat/ . The program was finished
successfully.
Here is my input mdin files.
&cntrl
irest=0,
nstlim=100,numexchg=10,
ntpr=100, ntwr=100,ntave=100,
nscm=100,ntwx=100,
dt=0.001, vlimit=10.0,
cut=12.,imin=0,
ntt=1,
temp0=XXXXX, ig=RANDOM_NUMBER,
tautp=0.5,
iamoeba=1
&end
&ewald
nfft1=36,nfft2=36,nfft3=36,
skinnb=0.8,nbtell=0,order=5,ew_coeff=0.45,
&end
&amoeba
do_induced=1,do_recip=1,do_direct=1,do_adjust=1,
do_amoeba_nonbond=1,do_amoeba_valence=1,beeman_integrator=1,
do_bond=1,do_ureyb=1,do_reg_angle=1,do_trig_angle=1,
do_opbend=1,do_torsion=1,do_str_torsion=1,do_pi_torsion=1,do_strbend=1,
do_torsion_torsion=1,amoeba_verbose=0,
do_vdw=1,do_vdw_longrange=1,do_vdw_taper=1,
do_self=1,dipole_scf_tol = 0.01,dipole_scf_iter_max=30,
sor_coefficient=0.7,ee_damped_cut=4.5,ee_dsum_cut=6.8,
&end
Remd.groupfile
-O -rem 1 -remlog rem.log -i remd.mdin.001 -o remd.mdout.001 -c
equilibrate.rst.001 -r remd.rst.001 -x remd.mdcrd.001 -inf remd.mdinfo.001
-p lig_h_wat.prmtop
-O -rem 1 -remlog rem.log -i remd.mdin.002 -o remd.mdout.002 -c
equilibrate.rst.002 -r remd.rst.002 -x remd.mdcrd.002 -inf remd.mdinfo.002
-p lig_h_wat.prmtop
-O -rem 1 -remlog rem.log -i remd.mdin.003 -o remd.mdout.003 -c
equilibrate.rst.003 -r remd.rst.003 -x remd.mdcrd.003 -inf remd.mdinfo.003
-p lig_h_wat.prmtop
-O -rem 1 -remlog rem.log -i remd.mdin.004 -o remd.mdout.004 -c
equilibrate.rst.004 -r remd.rst.004 -x remd.mdcrd.004 -inf remd.mdinfo.004
-p lig_h_wat.prmtop
Run_remd
mpirun -n 4 sander.MPI -ng 2 -groupfile remd.groupfile > remd.out &
Does anyone know what my problem is? Or AMOEBA10 still does not support REMD
with AMOEBA?
Thanks in advance for your help!
Yue
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Received on Thu May 27 2010 - 16:00:04 PDT
