Hello,
I am having trouble running Amoeba simulations in the latest pmemd.gem coupled with nmropt=1 (for umbrella sampling/WHAM calculations).
When trying to run a simple minimization (the input file is attached below), simulation stops immediately with "No Amoeba support for file redirections!". When I moved the &rst section inside the mdin, another error occured: "No Amoeba support for &rst namelist-based options!".
Here is the input:
ala-ala umbrella sampling
&cntrl
imin=1, cut=8.0,
maxcyc=20000,
ntx=1,
ntf=1, ntc=1,
ntb=1,
iamoeba = 1,
nmropt = 1,
/
&ewald
order = 5,
ew_coeff=0.45,
nfft1=40,
nfft2=40,
nfft3=40,
/
&amoeba
beeman_integrator=1,
ee_dsum_cut = 7.0,
dipole_scf_tol = 0.0001,
dipole_scf_iter_max = 30,
/
&wt type='DUMPFREQ', istep1=10 /
&wt type='END' /
DISANG=di_-180.-180.rst
DUMPAVE=di_vs_t.-180.-180
The RST file is:
# torsion restraints for phi/psi
&rst
iat=11,13,15,21, r1=-350., r2=-180., r3=-180., r4=10., rk2 = 25.,
rk3 = 25., /
&rst
iat=1,5,11,13, r1=-350., r2=-180., r3=-180., r4=10., rk2 = 25.,
rk3 = 25., /
I have tried to run these with both pmemd.gem and pmemd.gem.MPI. Beeman integrator is =1 for I plan to use MC barostat for the production run.
Is there some known way how to circumvent this problem?
Here I found a similar issue being discussed, but regarding pmemd.amoeba (
http://archive.ambermd.org/201506/0083.html).
Thanks a lot in advance.
With regards,
Lubos Plamitzer
Student / Biomolecular Spectroscopy
T +420 220 183 130 | M +420 776 888 002
lubos.plamitzer.uochb.cas.cz
Institute of Organic Chemistry and Biochemistry of the CAS
Flemingovo nám. 2 | 166 10 Praha 6 | Czech Republic
www.iocb.cz | facebook.com/IOCBPrague
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Received on Sat Jul 27 2019 - 13:00:02 PDT
