[gmx-users] Hydroxyapatite MD odd behavior

Justin Lemkul jalemkul at vt.edu
Wed Jul 25 21:10:43 CEST 2012

On 7/25/12 2:32 PM, Ramon Garduno wrote:
> Dear gmx friends:
> We are modeling a solvated hydroxyapatite(HAP)-protein complex. We have
> minimized and equilibrated this system to 300K under NVT.
> The odd behavior is observed when we start an NPT simulation. In the very
> first ps we observed that the oxygens bound (initially) to phosphorous in
> phosphate tetrahedon assume a geometry in which all four oxygens are grouped
> together like this P=O, however we never receive an error message.
> The bond lenghts have been constrained using the SHAKE algorithm.
> HAP is in the form of a crystal slab. The HAP parameters we have used were
> taken from Dinesh-Katti's paper [Polymer 48 (2007) 664-674], in turn, Katti
> took the HAP parameters from Hauptmann [Phys Chem Chem Phys  (2003) 5, 635-639].
> Katti's parameters were parameterized to CVFF. We have made ​​the
> corresponding unit convertions to fit those requiered in GROMACS v4.5. In
> short, we have used NON_BONDED (Homonuclear and Heteronuclear van der Waals
> terms), BONDED parameters (ffnonbonded.itp and HAP.itp), and the same PARTIAL
> ATOMIC CHARGES as those reported by Katti's group.
> In order to avoid the odd behaviour observed in the tetrahedral phosphate, we
> have used strong position restraints but the odd behaviour is still present.
> We also used freeze groups but with this command it is not possible to
> equilibrate the system under NPT.
> Do you have some suggestions to solve this problem?

It sounds like a topology error, but without seeing the .itp file, it's hard to 



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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