VMD-L Mailing List

From: hamid mosaddeghi (hamid592004m_at_yahoo.com)
Date: Wed Aug 31 2011 - 12:28:09 CDT

Dear Axel   I used same condition with some paper and then I have this problem.   do you write HBOND tcl in VMD? Please check it for SPC/E water.   PS: my systems run under Dl_poly 2.18 and after equilibrated I used History file for analysis. condition of my system:   -temperature: 300K -Pressure: 1-3 atm -density: 0.998 g/cm3 -timestep:0.001 ns -I used Spc/e water with constraint see help dl_poly    Best Regards From: Axel Kohlmeyer <akohlmey_at_gmail.com> To: hamid mosaddeghi <hamid592004m_at_yahoo.com> Cc: vmd <vmd-l_at_ks.uiuc.edu> Sent: Wednesday, August 31, 2011 5:15 PM Subject: Re: vmd-l: Hbond in VMD On Wed, Aug 31, 2011 at 4:12 AM, hamid mosaddeghi <hamid592004m_at_yahoo.com> wrote: > Dear all > > I counted Hbond from VMD for SPC/E water model in normal condition , I got > 2.56 Hbond per/molcule but more paper reported 3.~ 3.3 Hbond per/molcule > why? there are a _ton_ of possible reasons. > I used Cutoff angle 30 and cutoff distance 3.5 A from literatures. that still doesn't mean you are using the exact same definition of hydrogen bonds, and more importantly, it doesn't say anything about whether your simulation has been properly equilibrated and is simulating the exact same region in phase space. did you do any statistical error estimates? axel. > Best regards > > Hamid Mosaddeghi > > Phd Student Of Physical Chemistry -- Dr. Axel Kohlmeyer akohlmey_at_gmail.com  http://goo.gl/1wk0 Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.