Re: [gmx-users] Donors and Acceptors - gmx hbond - gromacs.org_gmx-users Digest, Vol 160, Issue 67

[Marcelo Depólo]

Hi Mark,


I've tried your suggestion. I've made an index file with my oxygen (O) and
my hydroxyl group (OH). Here my results:

H-bond average (calculated using num.xvg):
O = 1.10 +/- 0.62
OH = 2.06 +/- 0.66

(The first line from .log for each group)
# DonorHydrogen  Acceptor
O=  SOL2OW  SOL2HW1  MET1O
OH =   MET1O MET1HHSOL2OW

My command line for each group was:

gmx_507 hbond -s met.SIM.tpr -f met.SIM-traj.xtc -n wat_ana.ndx -shell 0.5
-r 0.35 -a 30 -num met.num.xvg -hbn met.hbn.ndx -don met.donors.xvg -dan
met.dan.xvg -g met.log

So I am a bit confused. I was expecting only 1 H-bond from OH group (since
O is able to donate only one H), and 2 H-bonds accepted for O. Based on the
.log, gmx hbond doesn't seem to be calculating H-bond for acceptors and
donors at the same time, what would justify this value of 2 for OH (1
accepted and 1 donated).

So, I ran out of ideas. Does anyone have any? Does these values make sense?

Cheers!
Marcelo

--
>
> Message: 2
> Date: Mon, 14 Aug 2017 12:13:38 +
> From: Mark Abraham <mark.j.abra...@gmail.com>
> To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] Donors and Acceptors - gmx hbond
> Message-ID:
> <CAMNuMAQ2LLXpSQ1ChMoKiBd-YJP4s+76Dou0Wvn5sLmj_UGJng@
> mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> I would use the selection groups judiciously, for example have one of them
> with only donor atoms in it.
>
> Mark
>
>
-- 
--
Marcelo Depólo Polêto
DSc. Cell and Molecular Biology - UFRGS (Brazil)
Group of Structural Bioinformatics - Room 202
Center of Biotechnology - UFRGS
Phone: + 55 51 3308-7770
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Re: [gmx-users] Donors and Acceptors - gmx hbond

[Mark Abraham]

Hi,

I would use the selection groups judiciously, for example have one of them
with only donor atoms in it.

Mark

On Fri, 11 Aug 2017 00:05 Marcelo Depólo  wrote:

> Hi all!
>
>
> I've been wondering how donors and acceptors are defined in gmx hbond. In
> the help output:
>
> "(...) OH and NH groups are regarded as donors, O is an acceptor always, N
> is an acceptor by default, but this can be switched using -nitacc. Dummy
> hydrogen atoms are assumed to be connected to the first  preceding
> non-hydrogen atom.
>
> You need to specify two groups for analysis, which must be either identical
> or
> non-overlapping. All hydrogen bonds between the two groups are analyzed."
>
> So if I evaluate a 'OH' group (in MeOH - water solution, for example), will
> I be calculating the h-bonds donated by H atom and accepted by the O atom
> at the same time? If so, is there anyway to calculate both separately?
>
> Cheers!
> --
> Marcelo Depólo Polêto
> DSc. Cell and Molecular Biology - UFRGS (Brazil)
> Group of Structural Bioinformatics - Room 202
> Center of Biotechnology - UFRGS
> Phone: + 55 51 3308-7770
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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[gmx-users] Donors and Acceptors - gmx hbond

[Marcelo Depólo]

Hi all!


I've been wondering how donors and acceptors are defined in gmx hbond. In
the help output:

"(...) OH and NH groups are regarded as donors, O is an acceptor always, N
is an acceptor by default, but this can be switched using -nitacc. Dummy
hydrogen atoms are assumed to be connected to the first  preceding
non-hydrogen atom.

You need to specify two groups for analysis, which must be either identical
or
non-overlapping. All hydrogen bonds between the two groups are analyzed."

So if I evaluate a 'OH' group (in MeOH - water solution, for example), will
I be calculating the h-bonds donated by H atom and accepted by the O atom
at the same time? If so, is there anyway to calculate both separately?

Cheers!
--
Marcelo Depólo Polêto
DSc. Cell and Molecular Biology - UFRGS (Brazil)
Group of Structural Bioinformatics - Room 202
Center of Biotechnology - UFRGS
Phone: + 55 51 3308-7770
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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