Aw: Re: [gmx-users] the "-dist" flag of g_hbond tool

2013-05-24 Thread lloyd riggs
r GROMACS users" Betreff: Re: [gmx-users] the "-dist" flag of g_hbond tool It used to be. I didn't realise it was still in the code. We experimented a bit with having a continuous bond criterion instead of a binary measure. It didn't do for us what we hoped it would so i

Re: [gmx-users] the "-dist" flag of g_hbond tool

2013-05-24 Thread Erik Marklund
It used to be. I didn't realise it was still in the code. We experimented a bit with having a continuous bond criterion instead of a binary measure. It didn't do for us what we hoped it would so it was abandoned. I know that some people are using Espiniozas empirical formula for bond energy, how

Re: [gmx-users] the "-dist" flag of g_hbond tool

2013-05-24 Thread CHEN Pan
Yes. I have looked at it already. I may need to spend time to understand it. By the way, in the source code, it seems some part are written for calculating hydrogen bonding energy, but I haven't see any "flag command" could give a output of "hydrogen bonding energy" file. Is it still under develop

Re: [gmx-users] the "-dist" flag of g_hbond tool

2013-05-24 Thread Erik Marklund
Hm. That is peculiar. The source code has the answer of course. I can have a look next week to see why that is. Erik On 24 May 2013, at 14:11, CHEN Pan wrote: > Hi, > > I have 512 donors and 1024 acceptors. > > I have just tested "g_hbond" with my standard crystal structure, which I > should

Re: [gmx-users] the "-dist" flag of g_hbond tool

2013-05-24 Thread CHEN Pan
Hi, I have 512 donors and 1024 acceptors. I have just tested "g_hbond" with my standard crystal structure, which I should get 512 hydrogen bonds. And the output "hbnum.xvg" does show 512 hydrogen bonds, which is correct. But the "hbdist.xvg" file still shows that the summation of population is 20

Re: [gmx-users] the "-dist" flag of g_hbond tool

2013-05-24 Thread Erik Marklund
Hi, See below On 24 May 2013, at 11:45, CHEN Pan wrote: > Dear Gromacs users, > > I am confused about the g_hbond tools. > > 1) When I use "-dist" to get the distribution of hydrogen bonding distance, > I found that the summation of the population is always 200 (the y-column > below). I am no

[gmx-users] the "-dist" flag of g_hbond tool

2013-05-24 Thread CHEN Pan
Dear Gromacs users, I am confused about the g_hbond tools. 1) When I use "-dist" to get the distribution of hydrogen bonding distance, I found that the summation of the population is always 200 (the y-column below). I am not sure if it's was done with normalization or not, if yes, the summation s