[gmx-users] Normal Mode Analysis in Double-Precision
Ran Friedman
r.friedman at bioc.uzh.ch
Thu Jul 31 16:47:23 CEST 2008
Ran Friedman wrote:
> Inon Sharony wrote:
>
>> 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?)
>>
> When you run gmxdump it should right e.g.:
>
correction: Should WRITE.
> Reading file em.tpr, VERSION 3.3.3 (double precision)
>
> As for the coordinates, you have e.g.:
> x[ 0]={ 1.35920e+01, 1.80590e+01, 1.79780e+01}
> x[ 1]={ 1.31410e+01, 1.77710e+01, 1.75260e+01}
> x[ 2]={ 1.30070e+01, 1.78390e+01, 1.68430e+01}
>
> This is double precision. In single precision you'd get only 3 digits,
> and the rest will be zeroes.
>
>> 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?
>>
> It doesn't matter if you use pdb or gro. step*.pdb files are sometimes
> given in the output when the system explodes.
>
> It can be that the parameters from PRODRG are not exactly what you want
> - you should compare with the force field paramters and charges, though
> I'm not sure this can be the source of this behaviour.
>
>> 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...
>>
> I'm not sure a diatomic system is good for this - not enough degrees on
> freedom.
> I'll send you an example made with GMX 3.2.1 - I'm not doing NMA too
> often, but it should work.
>
>> Thanks very much again,
>>
>> Inon.
>>
>>
>> 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
>>>>
>> 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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>> posting!
>>
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>>>
>> --Inon Sharony
>> ×™× ×•×Ÿ ×©×¨×•× ×™
>> +972(3)6407634
>> atto.TAU.ac.IL/~inonshar
>> Please consider your environmental responsibility before printing
>> this e-mail.
>>
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>>
>
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--
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman
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