[gmx-users] Hydroxyapatite MD odd behavior
ramon at fis.unam.mx
Wed Aug 8 00:51:16 CEST 2012
Thank you Justing...
We are working on your observations...
We are sure that we will get back on this issue as soon as we figure out what
we have done wrong...
On Mon, 06 Aug 2012 15:29:04 -0400, Justin Lemkul wrote
> 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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