[gmx-users] multi file input for index files
tsjerkw at gmail.com
Tue Jan 10 12:16:15 CET 2012
In cases where you do end up with two index files, like resulting from
a script or so, you can also simply combine them by concatenation:
cat A.ndx B.ndx > C.ndx
Of course you'll have to make sure that the group names are unique ;)
2012/1/10 ahmet yıldırım <ahmedo047 at gmail.com>:
> Thanks Mark and Marzinek,
> The Problem is solved:
> g_hbond -f traj.xtc -s run.tpr -num AB.xvg -n AB.ndx
>> chain A
> Found 1234 atoms with chain identifier A
> 19 chA : 1234 atoms
>> name 19 chainA
>> chain B
> Found 1234 atoms with chain identifier B
> 20 chB : 1234 atoms
>> name 20 chainB
> 2012/1/10 Marzinek, Jan <j.marzinek10 at imperial.ac.uk>
>> So as you can see Gromacs does not support multi file input :) Create one
>> index file and specify there your two groups. Then g_hbond will ask you to
>> choose two groups from this file.
>> Jan Marzinek
>> PhD Candidate
>> Centre for Process Systems Engineering
>> Department of Chemical Engineering
>> Imperial College London
>> South Kensington Campus
>> London SW7 2AZ
>> E: j.marzinek10 at imperial.ac.uk
>> M: +44(0)7411 640 552
>> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on
>> behalf of ahmet yıldırım [ahmedo047 at gmail.com]
>> Sent: Tuesday, January 10, 2012 8:13 AM
>> To: Discussion list for GROMACS users
>> Subject: [gmx-users] multi file input for index files
>> Dear users,
>> I created two different index files (A.ndx and B.ndx). I want to run the
>> two files at the same time.
>> g_hbond -f traj.xtc -s run.tpr -num A-B.xvg -n A.ndx -n B.ndx
>> where, I want to calculate the hydrogen bonds between A and B.
>> This command is giving the error as it expected. "Gromacs tools do not
>> support multi file input for index files" from
>> Is this correct? If no, what should I do?
>> Thanks in advance
>> Ahmet Yıldırım
>> gmx-users mailing list gmx-users at gromacs.org
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> Ahmet Yıldırım
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Tsjerk A. Wassenaar, Ph.D.
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
More information about the gromacs.org_gmx-users