Hard to tell from your descriptions. Things to consider: 1) Is the force-field for the ZnO particle realistic (have you validated it or have evidence that it is accurate) 2) If the ZnO particle has a net charge and you are running PME you are going to need to neutralize the system such that it accounts for both the protein and the ZnO nanoparticle 3) Why do you think it is wrong? What experimental evidence can you compare to benchmark if your results are reasonable?
We can't tell you if your results are "right or wrong," that's your responsibility to know this and justify it before submitting to review, but the questions above may help drive your thinking a bit on this. Hope that helps. =================== Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Hassan Aaryapour <hassan.grom...@gmail.com> Sent: Wednesday, February 21, 2018 3:47 AM To: gromacs.org_gmx-users; gmx-us...@gromacs.org Subject: [gmx-users] ZNO-HSA (Human Serum albumin) Interaction Dear Gromacs Users; I am studying the toxicity effect of ZnO nanoparticle (with a partial charges of +1.026 and -1.026 for Zinc and Oxygen atoms, respectively) on the Albumin structure by Gromacs. For MD simulation the nanoparticle was placed at a distance of 1nm of protein, after running pdb2gmx, the simulation box was solvated by TIP3P waters. The net charge of protein in physiological condition is -14 that was neutralized by adding sodium and chloride ions to box. Then, energy minimization, NVT and NPT were done. >From the beginning of md simulation, the protein structure began to be unfolded slowly before binding nanoparticle to it and after binding, the protein structure changed dramatically. I cannot consider the charge of ZnO as zero like silver or gold nanoparticles. So, I am confused that whether the study method is correct or wrong for this interaction? Do the results seem logical? Thanks Hassan Aryapour -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
