[gmx-users] Normal Mode Analysis in Double-Precision
InonShar at post.TAU.ac.IL
Thu Jul 31 16:04:15 CEST 2008
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.,
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,
Quoting "Ran Friedman" <r.friedman at bioc.uzh.ch>:
> Inon Sharony wrote:
>> Hi Ran, thanks for the reply
>> I ran "make tests" after compiling with double precision, and it
>> out fine.
>> Could it be that this, second, compilation might have caused some
>> problems -- I had GROMACS compiled in single-precision, and it
>> 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,
>> but I get the segfault from mdrun (also in double-precision).
>> Sometimes this happens in the first minimization step, and
>> in the second. I was told that this might hint that the input
>> (e.g. the *.gro file) were input in single- and not
>> However, since the files have coordinates written in nanometers to
>> four significant digits, I can't see how the input numbers could
>> single or double precision. It was suggested that I insert a
>> screen" line in the source code immediately after the *.gro file
>> 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
> with gmxdump.
> Other things that you may want to consider:
> 1. Do you get step*.pdb files after running mdrun? This may point
> something wrong in the input.
> 2. Are you using a solvated system? Normally NMA is done in vacuo,
> with some scaling of the dielectric.
> 3. Did you examine the system that you use in the input? Does it
> sense to you?
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