Dear Rachel,
did you apply bugfix.7 for amber8? There was a bug in selections using
distance criteria and it wouldn't work for either opteron or itanium.
The best way to check if the selection works (especially for more
complicated mask expressions) is to use utility 'ambmask' (see amber8
manual for syntax and usage) to generate pdb file with selected atoms
and check if it picked the atoms you wanted (or even visualize them if
the selection is more complicated, e.g. involving distance comparisons).
It might be tricky to use 'ambmask' and avoid shell expansions for the
mask expression, but it should be possible to do.
If you're absolutely sure that restrained atoms were picked correctly on
opteron (did you use the same compiler on the opteron, i.e. Intel 8.1?)
but not on itanium, I would need your help to generate some debug
information from 'ambmask'...
Cheers,
-Viktor
Rachel Burdge wrote:
>Amber Users,
>
>I have successfully run MD with restrained atoms on an amd64 opteron and
>i686 machines. However, when I run the same exact set of files on an
>ia64 itanium the restrained atoms are not recognized, but the simulation
>continues with no other errors. Has anyone experienced similar problems
>using restraints?
>
>Amber was compiled using the 64-bit Intel compilers (configuration
>option ia64_ifort):
>
>Intel(R) C++ Itanium(R) Compiler for Itanium(R)-based applications
>Version 8.1 Build 20040922 Package ID: l_cc_pc_8.1.022
>Intel(R) Fortran Itanium(R) Compiler for Itanium(R)-based applications
>Version 8.1 Build 20040922 Package ID: l_fc_pc_8.1.019
>
>Thank you-
>Rachel Burdge
>Washington University in St. Louis
>
>Input file is shown below:
>
>
>LOADING THE CONSTRAINED ATOMS AS GROUPS
>
>
> Mask :* & !:2855<:20.0; matches 0 atoms
>
>
>Here is the input file:
>
> &cntrl
>
> nmropt = 0,
> ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
> ntpr = 50, ntwx = 500, ntwv = 0, ntwe = 0,
>
>
> ntf = 1, ntb = 0,
> cut = 40.0, nsnb = 10,
>
> ibelly = 0, ntr = 1, igb = 5, saltcon = 0.2,
> restraint_wt = 10,
> restraintmask = ':* & !:2855<:20.0 & !:WAT',
>
>
> imin = 0,
> nstlim = 5000,
> nscm = 500,
> t = 0.0, dt = 0.002,
>
> temp0 = 50.0, tempi = 50.0,
> ntt = 3,
> gamma_ln = 5,
>
> ntp = 0,
>
> ntc = 2,
>
> &end
>
>
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Received on Thu Feb 17 2005 - 23:53:00 PST
