Re: [gmx-users] question about g_hbond

2013-09-01 Thread Justin Lemkul
On 9/1/13 1:30 PM, Nidhi Katyal wrote: I have created my files long time ago using version 4.0.7. But now analyzing the same files using g_hbond/g_mindist using version 4.5.5 Try 4.6.3. If it still doesn't work, you can feel free to file a bug report on redmine.gromacs.org, or otherwise ju

Re: [gmx-users] question about g_hbond

2013-09-01 Thread Nidhi Katyal
I have created my files long time ago using version 4.0.7. But now analyzing the same files using g_hbond/g_mindist using version 4.5.5 On Sun, Sep 1, 2013 at 10:48 PM, Justin Lemkul wrote: > > > On 9/1/13 1:17 PM, Nidhi Katyal wrote: > >> Even after giving same cutoff radius of 0.35nm in both,

Re: [gmx-users] question about g_hbond

2013-09-01 Thread Justin Lemkul
On 9/1/13 1:17 PM, Nidhi Katyal wrote: Even after giving same cutoff radius of 0.35nm in both, I am getting around 400 contacts per timeframe with mindist but 0 contacts with g_hbond. What version of Gromacs are you using? -Justin On Sun, Sep 1, 2013 at 10:40 PM, Justin Lemkul wrote:

Re: [gmx-users] question about g_hbond

2013-09-01 Thread Nidhi Katyal
Even after giving same cutoff radius of 0.35nm in both, I am getting around 400 contacts per timeframe with mindist but 0 contacts with g_hbond. On Sun, Sep 1, 2013 at 10:40 PM, Justin Lemkul wrote: > > > On 9/1/13 1:08 PM, Nidhi Katyal wrote: > >> The two groups are: protein and cosolvent mo

Re: [gmx-users] question about g_hbond

2013-09-01 Thread Justin Lemkul
On 9/1/13 1:08 PM, Nidhi Katyal wrote: The two groups are: protein and cosolvent molecules. With g_mindist -on , I am getting values of around 6500 per timeframe. But then why g_hbond giving different results. Are you using the same cutoff radius for both? -Justin On Sun, Sep 1, 2013 at

Re: [gmx-users] question about g_hbond

2013-09-01 Thread Nidhi Katyal
The two groups are: protein and cosolvent molecules. With g_mindist -on , I am getting values of around 6500 per timeframe. But then why g_hbond giving different results. On Sun, Sep 1, 2013 at 10:23 PM, Justin Lemkul wrote: > > > On 9/1/13 12:50 PM, Nidhi Katyal wrote: > >> Hello, >> I would

Re: [gmx-users] question about g_hbond

2013-09-01 Thread Justin Lemkul
On 9/1/13 12:50 PM, Nidhi Katyal wrote: Hello, I would like to calculate number of contacts between two groups, for which I am using following command: g_hbond -f *.xtc -s *.tpr -num *.xvg -contact -b 49000 -e 5 I am getting 0 as the output. But when I am calculating number of hydrogen bond

[gmx-users] question about g_hbond

2013-09-01 Thread Nidhi Katyal
Hello, I would like to calculate number of contacts between two groups, for which I am using following command: g_hbond -f *.xtc -s *.tpr -num *.xvg -contact -b 49000 -e 5 I am getting 0 as the output. But when I am calculating number of hydrogen bonds between the same two groups by using the a

Re: [gmx-users] Question about g_hbond output

2010-08-13 Thread Justin A. Lemkul
Jinyao Wang wrote: Hi evergyone, I analysed the number of hydrogenation bond with Gromacs 4.0.4 by running g_hbond -s md.tpr -f md.xtc -num numhbond.xvg There are 3 columns in the output files. The first column = frame The second column = H bonds The third column = pairs within 0.

[gmx-users] Question about g_hbond output

2010-08-13 Thread Jinyao Wang
Hi evergyone, I analysed the number of hydrogenation bond with Gromacs 4.0.4 by running g_hbond -s md.tpr -f md.xtc -num numhbond.xvg There are 3 columns in the output files. The first column = frame The second column = H bonds The third column = pairs within 0.35nm The third colu