Hi Ran.
I looked up your suggestions, and got the following:
0. The parameters in the *.tpr file appear in " 0.00000000e+00 "
format. How can I tell if this is a float or double? Also, I could not
see if the position coordinates of the molecule appear in the *.tpr
file (and if so, if they are in double-precision). Where do the
coordinates appear? (in the *.gro file only?)
1. I do not get any step*.pdb files after the mdrun. In fact, I skip
the *.pdb file altogether (using PRODRG). Could this be a problem?
2. The simulation is done in vacuo.
3. I examined the input *.gro file (as well as the single-precision
mdruns) using ngmx, and it looks great for those runs that work (i.e.,
single precision).
I will now try repeating the whole minimization-NormalMode process for
a simple diatomic, to see if I have any problems. Could you send a
working set of files for me to compare with? Assuming you've run
Normal Mode analyses in the past...
Thanks very much again,
Inon.
Quoting "Ran Friedman" <[EMAIL PROTECTED]>:
Inon Sharony wrote:
Hi Ran, thanks for the reply
I ran "make tests" after compiling with double precision, and it
came
out fine.
Could it be that this, second, compilation might have caused some
problems -- I had GROMACS compiled in single-precision, and it
worked
fine -- could compiling in double-precision after the initial
single-precision overrun some files? I'm not sure anymore...
Also, the grompp in double-precision works fine (no warnings,
etc.)
but I get the segfault from mdrun (also in double-precision).
Sometimes this happens in the first minimization step, and
sometimes
in the second. I was told that this might hint that the input
file/s
(e.g. the *.gro file) were input in single- and not
double-precision.
However, since the files have coordinates written in nanometers to
four significant digits, I can't see how the input numbers could
be in
single or double precision. It was suggested that I insert a
"print to
screen" line in the source code immediately after the *.gro file
is
read, to see if the printed data is in single-precision or
double-precision format. What do you think?
The tpr should contain the data in double precision. You can check
this
with gmxdump.
Other things that you may want to consider:
1. Do you get step*.pdb files after running mdrun? This may point
out to
something wrong in the input.
2. Are you using a solvated system? Normally NMA is done in vacuo,
maybe
with some scaling of the dielectric.
3. Did you examine the system that you use in the input? Does it
make
sense to you?
Ran.
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