VMD-L Mailing List
From: hamid mosaddeghi (hamid592004m_at_yahoo.com)
Date: Mon Mar 07 2011 - 09:06:20 CST
- Next message: Peter Freddolino: "Re: Re: namd-l: hBond colvars and patching"
- Previous message: Francesco Pietra: "Re: namd-l: hBond colvars and patching"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
Dear all
I work with bulk water (SPC/E) and need to calculate Hbond, I used VMD
for this purpose,
for calculation Hbond (extention ----> Hydrogen .... ---->find
hydrogrn bond) I used cutoff angle
30 and cutoff distance 3.5.
then I calculate (number of hbond)/(number of water moleclue)= 1.27 ,
then I multiply it in 2
(beacause hbond share between two water molecule) ,then it equal ~2.6
but it is small of data
reported in paper for spc/e water (3.2) why? please help me.
if I used cutoff angle 45 instead 30 ,I get it equal=3.2 , is it correct?
what maximum cutoff angle?
thanks in advance
- Next message: Peter Freddolino: "Re: Re: namd-l: hBond colvars and patching"
- Previous message: Francesco Pietra: "Re: namd-l: hBond colvars and patching"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]