Re: [gmx-users] about g_hbond

2013-01-11 Thread Justin Lemkul
On 1/11/13 1:10 PM, Miguel Ángel Mompeán García wrote: The donors are two H atoms from the amide group of Gln residues. Thus, I will try the -merge option. Thank for the comment. I wonder if the following issue is affecting gromacs 4.5.5: http://lists.gromacs.org/pipermail/gmx-users/2011-May/

Re: [gmx-users] about g_hbond

2013-01-11 Thread Miguel Ángel Mompeán García
The donors are two H atoms from the amide group of Gln residues. Thus, I will try the -merge option. Thank for the comment. I wonder if the following issue is affecting gromacs 4.5.5: http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html 2013/1/11, Justin Lemkul : > > > On 1/11/13 6:

Re: [gmx-users] about g_hbond

2013-01-11 Thread Justin Lemkul
On 1/11/13 6:23 AM, Miguel Ángel Mompeán García wrote: Hi all, When calculating the average number of hbonds during a simulation, does the program g_hbond contemplate the possibility of an atom involved in two hbond? If I visualize the structures with molden, setting the same cutoff criterion

Re: [gmx-users] about g_hbond

2011-05-12 Thread lina
I got it. I should have outputted the -hbn file. Thanks, On Thu, May 12, 2011 at 1:09 PM, lina wrote: > /* y-label: "Hydrogen Bond Index" */ > > is it relevant to the total number of hydrogen bonds? > > such as > /* XPM */ > /* x-label: "Time (ps)" */ > /* y-label: "Hydrogen Bond Index" */ > /

Re: [gmx-users] about g_hbond

2011-05-11 Thread lina
/* y-label: "Hydrogen Bond Index" */ is it relevant to the total number of hydrogen bonds? such as /* XPM */ /* x-label: "Time (ps)" */ /* y-label: "Hydrogen Bond Index" */ /* type:"Discrete" */ static char *gromacs_xpm[] = { A-b : "51 84 2 1", b-C : "51 95 2 1", 84, 95? Thanks, On We

Re: [gmx-users] about g_hbond

2011-05-11 Thread lina
On Wed, May 11, 2011 at 11:10 PM, Justin A. Lemkul wrote: > > > lina wrote: >> >> Hi, >> >> For group A, b, C. >> >> It's no doubt can get hb forming number between A-b, b-C. b-(A or C). >> >> But I don't know how to get the number of residues of b forming both >> with A and B at the same time. na

Re: [gmx-users] about g_hbond

2011-05-11 Thread Justin A. Lemkul
lina wrote: Hi, For group A, b, C. It's no doubt can get hb forming number between A-b, b-C. b-(A or C). But I don't know how to get the number of residues of b forming both with A and B at the same time. namely b-A&C, not with AC group. There's no direct way to do it, but from the output