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? I Look forward to receiving your comments. Best, Ramon Garduno Research Professor in Biophysics Universidad Nacional Autonoma de Mexico -- Open WebMail Project (http://openwebmail.org) -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
