[gmx-users] intrapeptide hbond existence map

ABEL Stephane 175950 Stephane.ABEL at cea.fr
Thu Feb 11 20:05:48 CET 2010

Ok thank you all for your suggestions

A bientot

> ABEL Stephane 175950 wrote:
>> Hi everybody,
>> I am doing some analysis of the interpeptidique hbonds (INTRHB) 
>> during the aggregation in beta fuof 4 heptapeptides in water
>> I have defined in a index file the Acceptor-Donor-Hydrogen atoms list 
>> for the 28 INTRHB like this
>> NH--CO
>> [intra_hbds]
>> 4 17 5
>> 18 26 19
>> 27 43 28
>> 44 52 45
>> 53 60 54
>> ....
>> to obtain the INTRHB existence map i used the command with gmx4.05
>> g_hbond_mpi -n 4_Peptide_53A6_hbonds.ndx -s 4_Peptide_53A6.tpr -f 
>> ./XTC/Whole_Traj_53A6Center.xtc -b 400000 -e 500000 -hbn 
>> 4_Peptide_53A6_hbonds_400_500ns_index -hbm 
>> 4_Peptide_53A6_hbonds_400_500ns_Map
>> The map show in the x and y axis the time and residue (up to 84). I 
>> have no idea what the figure means. The olot is stored here 
>> http://www.st-abel.com/Hbond_occupency.jpg
>> I want only to know if, for example, the Hbond_occupency for the 
>> group NH or CO of the residu 1
> The output file "-hbn 4_Peptide_53A6_hbonds_400_500ns_index" maps the 
> donor-acceptor pairs to the plot. Find within that index file a 
> directive that starts with "hbonds" that corresponds to all of the 
> H-bonds that were found, and thus plotted. Red indicates the H-bond 
> exists, white means it doesn't. As for occupancy, you'd probably have 
> to script that to parse the .xpm file and calculate a percentage of 
> frames for when the particular H-bond exists, or get lifetimes from 
> g_hbond.
> -Justin
.or to define smaller index groups, e.g. the NH- or CO-group of res 1, 
and get the number of hydrogen bonds as function of time from the -num 
output (default is hbnum.xvg). You would have to repeat this for all 
(reasonable combinations of) hbonding groups that you're interested in, 
which can result in maaany g_hbond executions. But if the number of 
groups are small, then it's certainly doable. It seems from your plot 
though, that scripted processing of the -hbm and -hbn output, as Justin 
suggests, is the way to go here. Make sure you're matching the index 
file to the xpm file in the right way! I've made mistakes in that area 


>> Thank you in advance for your help
>> Stephane

Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys


Message: 5
Date: Thu, 11 Feb 2010 09:49:42 -0800
From: Lum Nforbi <lumngwegia at gmail.com>
Subject: [gmx-users] Working with Reduced Units
To: gmx-users at gromacs.org
	<f7e1d8851002110949w126829c5y3f5f2859cef4528b at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi all,

       Please, can someone shed more light on how to set up reduced units in
an .mdp file? I have tried to this but it does not work. I set epsilon,
sigma and mass to 1 in my force field file as stated in section 2.3 of the
manual. I multiplied 300K temperature by 0.00831451 and divided by epsilon
to get a temperature in reduced units with value 2.5. I also calculated the
pressure of 1bar in reduced units as shown on Table 2.4 of the manual to get
a value of 0.0431 and included all of these in the .mdp file but this did
not work for me in the mdrun.
      Is this the right way to set up reduced units in gromacs? Please, help
me out.

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Message: 6
Date: Thu, 11 Feb 2010 18:40:10 +0000
From: Rebeca Garc?a Fandi?o <regafan at hotmail.com>
Subject: [gmx-users] different results in different machines
To: <gmx-users at gromacs.org>
Message-ID: <BAY142-W9AC927EB472E1C1568B58B74E0 at phx.gbl>
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