Dear Jason,
This is the method I used?
> > > As LCOD reaction coordinate is not available in AMBER10, I also
> > downloaded the code in the tutorial and followed the readme file to install
> > the LCOD-amber10.tgz file. In the $AMBERHOME/src/sander directory, I type
> > "tar xvfz /LCOD-amber10.tgz". In the same directory, I type "make sander".
> > In the $AMBERHOME/src/sander directory, I can see a number of related files
> > as follows:
> > >
> > >
> > >
> > > >>ls *colvar*
> > > _ncsu-colvar.f ncsu_colvar.mod _ncsu-colvar-utils.f
> > > ncsu-colvar.f ncsu-colvar.o ncsu-colvar-utils.f
> > > _ncsu-colvar-math.f _ncsu-colvar-type.f ncsu_colvar_utils.mod
> > > ncsu-colvar-math.f ncsu-colvar-type.f ncsu-colvar-utils.o
> > > ncsu_colvar_math.mod ncsu_colvar_type.mod
> > > ncsu-colvar-math.o ncsu-colvar-type.o
> > >
> > >
> > > Thus, I seems to me that it is installed already. However, when I run the
> > same input files I downloaded from the tutorial A10 by typing the following
> > command line in console
> > >
> > >
> > >
> > > " $AMBERHOME/exe/sander -O -i mdin -o test2.out -p mr.top -c restrt -r
> > test2.rst -x test2.mdcrd "
> > >
> > >
> > >
> > > Following error message appears in the test2.out file
> > >
> > >
> > >
> > >
> > ===============================================================================
> > >
> > > MR
> > > begin time read from input coords = 925.000 ps
> > >
> > > Number of triangulated 3-point waters found: 0
> > >
> > > Sum of charges from parm topology file = -0.00010000
> > > Forcing neutrality...
> > >
> > > ** NCSU-Error ** : CV type 'LCOD' is not supported so far (CV #1)
> > >
> > ===============================================================================
> > >
> > >
> > >
> > > It seems to me that sander still cannot recognize the LCOD command. Do
> > you think I still need to modify the input file below to get it work:
> > >
> > >
> > >
> > >
> > ==============================================================================
> > >
> > >
> > >
> > > Malonaldehyde: NCSU steered MD: LCOD rxn coord
> > > &cntrl
> > > imin = 0,
> > > irest = 1,
> > > ntx = 5,
> > > ntb = 0,
> > > cut = 999.0,
> > > tempi = 300.0,
> > > temp0 = 300.0,
> > > ntt = 3,
> > > gamma_ln = 1.0,
> > > ntf = 2, ntc = 2, tol = 0.00001,
> > > dt = 0.0005,
> > > ntpr = 50, ntwr=100, ntwx = 100,
> > > nstlim = 100000,
> > > ifqnt = 1,
> > > /
> > > &qmmm
> > > qmmask=':*',
> > > qmcharge=0,
> > > qm_theory='AM1',
> > > qmshake=0,
> > > writepdb=1,
> > > /
> > >
> > > ncsu_smd
> > >
> > > output_file = 'smd.txt'
> > > output_freq = 1000
> > >
> > > variable
> > > type = LCOD ! Linear Combination of Distance
> > > i = (8,9,7,9)
> > > r = (1.0,-1.0)
> > > path = (0.7,-0.7)
> > > harm = (1000.0)
> > > end variable
> > >
> > > end ncsu_smd
> > >
> > =======================================================================================
> > >
> > >
> > >
> > >
> > >
> > > CAt
> > >
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Received on Mon Aug 09 2010 - 07:30:07 PDT
