[gmx-users] R: Re: H-bond lifetime with g_hbond

Anna Marabotti anna.marabotti at isa.cnr.it
Wed Oct 12 12:09:09 CEST 2011

Dear all,
any other suggestions on how to operate with g_hbond in order to allow
convergence of the autocorrelation function (see message below)? 

Moreover, I have another question. On the same trajectories, I'm using
g_hbonds also to infer the contacts between the protein and the ligand (and
possibly infer van der Waals interactions). This is the command I used:

g_hbond -f protein-GLA_mdC.xtc -s protein-GLA_md.tpr -g
protein-GLA_md_vdw.log -contact -r 1.4 -num protein-GLA_md_vdwnum.xvg

The printout of the command is:
Select a group: 1
Selected 1: 'Protein'
Select a group: 15
Selected 15: 'GLA'
Checking for overlap in atoms between Protein and GLA
Calculating contacts between Protein (5935 atoms) and GLA (24 atoms)
Found 24 donors and 5935 acceptors
Making hbmap structure...done.
Reading frame       0 time    0.000   
Will do grid-seach on 6x6x4 grid, rcut=1.4
Last frame       3000 time 30000.000   
Found 38017 different contacts in trajectory
Found 0 different atom-pairs within hydrogen bonding distance
Average number of contacts per timeframe 0.000 out of 71220 possible

However, the .log file gives me a list of interactions such as:
#      Donor      Hydrogen      Acceptor
  GLA395O4       PRO35O
  GLA395O4       GLY36N
  GLA395O4       GLY36CA
  GLA395O4       GLY36HA1
  GLA395O4       GLY36HA2
  GLA395O4       GLY36C
  GLA395O4       GLY36O
  GLA395O4       ARG37N
  GLA395O4       ARG37H

Moreover, I found previously several hBonds in this trajectory, therefore, I
don't understand why the printout tells "Found 0 different atom-pairs within
hydrogen bonding distance" and "Average number of contacts per timeframe
0.000 out of 71220 possible". I also used flag -r2 instead of -r, but the
result is the same. Maybe this is a trivial question, but...what is the
correct way to use the flags -contact and -r (or -r2) within g_hbond

Thanks a lot

Message: 1
Date: Tue, 11 Oct 2011 10:25:32 -0400
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] H-bond lifetime with g_hbond
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4E9451DC.6010104 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Anna Marabotti wrote:
> Dear gmx-users,
> I have a protein with 5 different ligands. For each system I made 30ns 
> simulation and I calculated the lifetime of the H-bonds between protein 
> and ligand with the command:
> g_hbond -f traj.xtc -s topol.tpr -hbm hbmap.xpm -hbn hbond.ndx -ac 
> hbac.xvg -life hblife.xvg
> During all calculations, the printout of the command gave the same
> WARNING: Correlation function is probably not long enough
> because the standard deviation in the tail of C(t) > 0.001
> and as a matter of fact, the tail of C(t) (average C(t) over second half 
> of acf) reported below this warning was always > 0.001, generally 
> comprised between 0.45 and 0.74 with two exceptions: a value of 
> 0.02+/-0.03 and a value of 0.04+/-0.01.

The warning doesn't complain about the value of C(t), it is telling you that
standard deviation in the value is unacceptable.

> Therefore, I'm asking if the forward values considered as lifetimes are 
> reliable or not, and in case, what can I do to avoid this warning.

I can't directly comment on this, but it would seems as if the values are
adequately converged.


> Thank you very much and best regards
> Anna
> ____________________________________________________
> Anna Marabotti, Ph.D.
> Laboratory of Bioinformatics and Computational Biology
> Institute of Food Science, CNR
> Via Roma, 64
> 83100 Avellino (Italy)
> Phone: +39 0825 299651
> Fax: +39 0825 781585
> Email: anna.marabotti at isa.cnr.it <mailto:anna.marabotti at isa.cnr.it>
> Skype account: annam1972
> Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
> "When a man with a gun meets a man with a pen, the man with a gun is a 
> dead man"
> (Roberto Benigni, about Roberto Saviano)


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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