[gmx-users] Hydroxyapatite MD odd behavior

Justin Lemkul jalemkul at vt.edu
Mon Aug 6 21:29:04 CEST 2012

On 8/6/12 3:13 PM, Ramon Garduno wrote:
> On Mon, 06 Aug 2012 13:52:46 -0400, Justin Lemkul wrote
>> Please provide all the necessary files, including topologies and
>> modified force field files.  I don't have time to make and double-
>> check all of these files and it's better to use exactly the same
>> files you've been trying to use.
> Dear Justin,
> Thank you for your prompt response and willingness to help us...
> Since we do not have problems with the protein-water system, we decided to
> look closely to what happens with the slab during the NVT simulation. Thus, I
> have placed in http://www.fis.unam.mx/~ramon/CursoDF/HAP/ for download all the
> files we are using (at your request) to analyze the extrange behavior observed
> on the tetrahedral phosphate ion.
> Hopefuly your trained eyes can see what we can not...

Immediately there is a problem.  Your cutoff values in the .mdp files (which are 
incorrect for Gromos96 53A6) are larger than the size of the small system will 
permit, causing grompp to fail with a fatal error.  If you're overriding this 
error with -maxwarn, then you're trying to simulate an unreasonable system since 
it violates the minimum image convention.

If you're working with other systems that are larger or different, please 
provide those files instead.  I've already had to make a large number of 
corrections to these files (mostly in atom naming/capitalization) to get grompp 
to even run, so parsing out those errors is somewhat annoying.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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