[gmx-users] probability density map

[Erik Marklund]

… from g_hbond I mean.

On 23 Mar 2014, at 00:04, Erik Marklund <erik.marklund at chem.ox.ac.uk> wrote:

> Hi,
> 
> All you need is in the hbm and hbn output.
> 
> Best regards,
> Erik
> 
> 
> Erik Marklund, PhD
> Postdoctoral Research Associate
> 
> Department of Chemistry
> Physical & Theoretical Chemistry Laboratory
> University of Oxford
> South Parks Road
> Oxford
> OX1 3QZ
> 
> On 22 Mar 2014, at 07:08, pratibha <kapoorpratibha7 at gmail.com> wrote:
> 
>> Hi all,
>> 
>> I would like to create 2D probability density map of backbone hydrogen bonds
>> between two peptide residues. Is it possible to do so using gromacs? 
>> I have read that g_mdmat makes distance matrices consisting of the smallest
>> distance between residue pairs. Is it possible to use such a tool to serve
>> my purpose? It asks only one group for analysis, but I want my xaxis and
>> yaxis to contain two different peptide residues.
>> Also, let me know if such a thing is possible using some other tools as well
>> (not sure if volmap of vmd could be of any help)?
>> Thanks 
>> 
>> --
>> View this message in context: http://gromacs.5086.x6.nabble.com/probability-density-map-tp5015312.html
>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>> -- 
>> Gromacs Users mailing list
>> 
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> 
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.