Hello,
I would like to run a steered-MD calculation with amber, using several
distance constraints simultaneously (i.e. steered to decrease several
different distances at the same time). Is this possible? Or can there only
be 1 steered distance? When I attempt to submit such a run with the
below-listed input files, either the 1st constraint is accepted, and the
rest are ignored, or I get the following error:
----------
"application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0"
"In Jarzynsky runs, there must only one restrain, stopping program"
---------
I have set up the dist.rst file as such:
&rst iresid=1,
atnam(1)=CA,
atnam(2)=CB,
iat=1218,3141, r2=35.1, rk2=5000., r2a=30.0,
&end
&rst iresid=1,
atnam(1)=CA,
atnam(2)=CB,
iat=1511,3142, r2=35.0, rk2=5000., r2a=30.0,
&end
&rst iresid=1,
atnam(1)=CA,
atnam(2)=CB,
iat=1611,3143, r2=34.0, rk2=5000., r2a=30.0,
&end
etc... etc...
and my mdin file looks as such:
&cntrl
imin=0,
nstlim=200,
ntpr=50, ntwx=50,ntt=3, gamma_ln=5.0,
cut=20.0,
ntb=0, igb=5, saltcon=0.75,
ntx=1, ig=25555,
ntc=2, ntf=2,
dt=0.002,
tempi=300, temp0=300,
jar=1,
/
&wt type='DUMPFREQ', istep1=1, /
&wt type='END', /
DISANG=dist.rst
DUMPAVE=dist_vs_t
LISTIN=POUT
LISTOUT=POUT
many thanks for your help!!
Ewa Golas, MSc.,
PhD Candidate
University of Gdansk
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Received on Fri Aug 24 2012 - 09:00:03 PDT
