Re: [gmx-users] Re: g_analyze
On 11/12/13 8:33 AM, bharat gupta wrote: Thanks justin for your replies. I understood the g_analyze related data. I tired g_analyze to dump the structures as you said. But, I didn't find any switch that can be used to dump the structure in pdb format. Because that's not the function of g_analyze. Use trjconv -dump with a suitable index file (from g_select). -Justin On Tue, Nov 12, 2013 at 10:15 PM, Justin Lemkul wrote: On 11/11/13 6:56 PM, bharat gupta wrote: Hi, I tried g_select to dump the structure with the interacting water molecules, but I don't know know how to do that. I searched for some threads in the discussion but wasn't able to find anything related to my need. Can you explain how can I do that ? Start with g_select -select 'help all' and see what you can determine. Such selections are rather straightforward and have been explained several times on the list. If you need help, show us what you're doing and describe why it isn't what you want. It will ultimately save a lot of time. -Justin On Tue, Nov 12, 2013 at 7:39 AM, bharat gupta wrote: Sorry, I attached the wrong file . Here's the average file generate from one of the files I sent in my last mail. I used the command g_analyze -f hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file obtained from this command :- https://www.dropbox.com/s/sovzk40cudznfjw/hbond_115-water-avg.xvg Now, if you see, the graph (in previous mail) and average file, both correlates well. I have a doubt about interpreting the result from g_analyze. The value "7.150740e+00" implies that on average 7 hydrogen bonds are formed during the simulation time of 5ns to 10ns. What does then the average file or its graph tells ?? On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul wrote: On 11/11/13 4:06 AM, bharat gupta wrote: In addition to my previous question, I have another question about g_analyze. When I used the hbond.xvg file to get the average and plotted the average.xvg file I found that the average value is round 4 to 5 according to the graph. But g_analyze in its final calculation gives 7.150 as the average values... Here's the link for the graph and result of average value calculated by g_analyze :- std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 * 7.150740e+00 * 8.803173e-01 1.760635e-02 0.0620.163 SS2 1.490604e+00 1.164761e+00 2.329523e-02 0.4950.153 https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png Here's the link hbond.xvg file and its averaged file https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg Neither of these files produce output that corresponds to the PNG image above. Both files have values in 6-9 H-bond range and thus agree with the g_analyze output, which I can reproduce. I suspect you're somehow getting your files mixed up. -Justin On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta < bharat.85.m...@gmail.com> wrote: thank you informing about g_rdf... Is it possible to dump the structure with those average water molecules interacting with the residues. I generated the hbond.log file which gives the details but I need to generate a figure for this ?? On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul wrote: On 11/10/13 8:38 PM, bharat gupta wrote: But trjorder can be used to calculate the hydration layer or shell around residues ... Right ?? Yes, but I also tend to think that integrating an RDF is also a more straightforward way of doing that. With trjorder, you set some arbitrary cutoff that may or may not be an informed decision - with an RDF it is clear where the hydration layers are. -Justin On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul wrote: On 11/10/13 8:30 PM, bharat gupta wrote: Thanks for your reply. I was missing the scientific notation part. Now everything is fine. Regarding trjorder, it doesn't measure h-bonds but gives the water nearest to protein. I wouldn't try to draw any sort of comparison between the output of trjorder and g_hbond. If you want to measure H-bonds, there's only one tool for that. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/Searc
Re: [gmx-users] Re: g_analyze
Thanks justin for your replies. I understood the g_analyze related data. I tired g_analyze to dump the structures as you said. But, I didn't find any switch that can be used to dump the structure in pdb format. On Tue, Nov 12, 2013 at 10:15 PM, Justin Lemkul wrote: > > > On 11/11/13 6:56 PM, bharat gupta wrote: > >> Hi, >> >> I tried g_select to dump the structure with the interacting water >> molecules, but I don't know know how to do that. I searched for some >> threads in the discussion but wasn't able to find anything related to my >> need. Can you explain how can I do that ? >> >> > Start with g_select -select 'help all' and see what you can determine. > Such selections are rather straightforward and have been explained several > times on the list. If you need help, show us what you're doing and > describe why it isn't what you want. It will ultimately save a lot of time. > > -Justin > > > >> On Tue, Nov 12, 2013 at 7:39 AM, bharat gupta >> wrote: >> >> Sorry, I attached the wrong file . Here's the average file generate from >>> one of the files I sent in my last mail. I used the command g_analyze -f >>> hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file obtained >>> from this command :- >>> >>> https://www.dropbox.com/s/sovzk40cudznfjw/hbond_115-water-avg.xvg >>> >>> Now, if you see, the graph (in previous mail) and average file, both >>> correlates well. I have a doubt about interpreting the result from >>> g_analyze. The value "7.150740e+00" implies that on average 7 hydrogen >>> bonds are formed during the simulation time of 5ns to 10ns. What does >>> then >>> the average file or its graph tells ?? >>> >>> >>> >>> On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul wrote: >>> >>> On 11/11/13 4:06 AM, bharat gupta wrote: In addition to my previous question, I have another question about > g_analyze. When I used the hbond.xvg file to get the average and > plotted > the average.xvg file I found that the average value is round 4 to 5 > according to the graph. But g_analyze in its final calculation gives > 7.150 > as the average values... Here's the link for the graph and result of > average value calculated by g_analyze :- > > std. dev.relative deviation of > standard - cumulants from > those > of > set average deviation sqrt(n-1) a Gaussian > distribition > cum. 3 cum. 4 > SS1 * 7.150740e+00 * 8.803173e-01 1.760635e-02 0.0620.163 > > SS2 1.490604e+00 1.164761e+00 2.329523e-02 0.4950.153 > > https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png > > Here's the link hbond.xvg file and its averaged file > https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg > https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg > > > Neither of these files produce output that corresponds to the PNG image above. Both files have values in 6-9 H-bond range and thus agree with the g_analyze output, which I can reproduce. I suspect you're somehow getting your files mixed up. -Justin On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta < > bharat.85.m...@gmail.com> > wrote: > > thank you informing about g_rdf... > >> >> Is it possible to dump the structure with those average water >> molecules >> interacting with the residues. I generated the hbond.log file which >> gives >> the details but I need to generate a figure for this ?? >> >> >> >> On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul >> wrote: >> >> >> >>> On 11/10/13 8:38 PM, bharat gupta wrote: >>> >>> But trjorder can be used to calculate the hydration layer or shell >>> around residues ... Right ?? Yes, but I also tend to think that integrating an RDF is also a more >>> straightforward way of doing that. With trjorder, you set some >>> arbitrary >>> cutoff that may or may not be an informed decision - with an RDF it >>> is >>> clear where the hydration layers are. >>> >>> -Justin >>> >>> >>> >>> On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul >>> wrote: On 11/10/13 8:30 PM, bharat gupta wrote: > >Thanks for your reply. I was missing the scientific notation > part. > Now > > everything is fine. >> >> Regarding trjorder, it doesn't measure h-bonds but gives the water >> nearest >> to protein. >> >> >>I wouldn't try to draw any sort of comparison between the >> output >> of >>
Re: [gmx-users] Re: g_analyze
On 11/11/13 6:56 PM, bharat gupta wrote: Hi, I tried g_select to dump the structure with the interacting water molecules, but I don't know know how to do that. I searched for some threads in the discussion but wasn't able to find anything related to my need. Can you explain how can I do that ? Start with g_select -select 'help all' and see what you can determine. Such selections are rather straightforward and have been explained several times on the list. If you need help, show us what you're doing and describe why it isn't what you want. It will ultimately save a lot of time. -Justin On Tue, Nov 12, 2013 at 7:39 AM, bharat gupta wrote: Sorry, I attached the wrong file . Here's the average file generate from one of the files I sent in my last mail. I used the command g_analyze -f hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file obtained from this command :- https://www.dropbox.com/s/sovzk40cudznfjw/hbond_115-water-avg.xvg Now, if you see, the graph (in previous mail) and average file, both correlates well. I have a doubt about interpreting the result from g_analyze. The value "7.150740e+00" implies that on average 7 hydrogen bonds are formed during the simulation time of 5ns to 10ns. What does then the average file or its graph tells ?? On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul wrote: On 11/11/13 4:06 AM, bharat gupta wrote: In addition to my previous question, I have another question about g_analyze. When I used the hbond.xvg file to get the average and plotted the average.xvg file I found that the average value is round 4 to 5 according to the graph. But g_analyze in its final calculation gives 7.150 as the average values... Here's the link for the graph and result of average value calculated by g_analyze :- std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 * 7.150740e+00 * 8.803173e-01 1.760635e-02 0.0620.163 SS2 1.490604e+00 1.164761e+00 2.329523e-02 0.4950.153 https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png Here's the link hbond.xvg file and its averaged file https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg Neither of these files produce output that corresponds to the PNG image above. Both files have values in 6-9 H-bond range and thus agree with the g_analyze output, which I can reproduce. I suspect you're somehow getting your files mixed up. -Justin On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta wrote: thank you informing about g_rdf... Is it possible to dump the structure with those average water molecules interacting with the residues. I generated the hbond.log file which gives the details but I need to generate a figure for this ?? On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul wrote: On 11/10/13 8:38 PM, bharat gupta wrote: But trjorder can be used to calculate the hydration layer or shell around residues ... Right ?? Yes, but I also tend to think that integrating an RDF is also a more straightforward way of doing that. With trjorder, you set some arbitrary cutoff that may or may not be an informed decision - with an RDF it is clear where the hydration layers are. -Justin On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul wrote: On 11/10/13 8:30 PM, bharat gupta wrote: Thanks for your reply. I was missing the scientific notation part. Now everything is fine. Regarding trjorder, it doesn't measure h-bonds but gives the water nearest to protein. I wouldn't try to draw any sort of comparison between the output of trjorder and g_hbond. If you want to measure H-bonds, there's only one tool for that. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.u
Re: [gmx-users] Re: g_analyze
On 11/11/13 5:39 PM, bharat gupta wrote: Sorry, I attached the wrong file . Here's the average file generate from one of the files I sent in my last mail. I used the command g_analyze -f hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file obtained from this command :- https://www.dropbox.com/s/sovzk40cudznfjw/hbond_115-water-avg.xvg Now, if you see, the graph (in previous mail) and average file, both correlates well. I have a doubt about interpreting the result from g_analyze. The value "7.150740e+00" implies that on average 7 hydrogen bonds are formed during the simulation time of 5ns to 10ns. What does then the average file or its graph tells ?? It's an average over sets. It is not equivalent to the output printed to the screen, nor is it supposed to. The value printed to the screen is the actual average of the data set of interest, as is intuitive from your values. An average of 4 is impossible if all the data points are in the range of 6-9. -Justin On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul wrote: On 11/11/13 4:06 AM, bharat gupta wrote: In addition to my previous question, I have another question about g_analyze. When I used the hbond.xvg file to get the average and plotted the average.xvg file I found that the average value is round 4 to 5 according to the graph. But g_analyze in its final calculation gives 7.150 as the average values... Here's the link for the graph and result of average value calculated by g_analyze :- std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 * 7.150740e+00 * 8.803173e-01 1.760635e-02 0.0620.163 SS2 1.490604e+00 1.164761e+00 2.329523e-02 0.4950.153 https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png Here's the link hbond.xvg file and its averaged file https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg Neither of these files produce output that corresponds to the PNG image above. Both files have values in 6-9 H-bond range and thus agree with the g_analyze output, which I can reproduce. I suspect you're somehow getting your files mixed up. -Justin On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta wrote: thank you informing about g_rdf... Is it possible to dump the structure with those average water molecules interacting with the residues. I generated the hbond.log file which gives the details but I need to generate a figure for this ?? On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul wrote: On 11/10/13 8:38 PM, bharat gupta wrote: But trjorder can be used to calculate the hydration layer or shell around residues ... Right ?? Yes, but I also tend to think that integrating an RDF is also a more straightforward way of doing that. With trjorder, you set some arbitrary cutoff that may or may not be an informed decision - with an RDF it is clear where the hydration layers are. -Justin On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul wrote: On 11/10/13 8:30 PM, bharat gupta wrote: Thanks for your reply. I was missing the scientific notation part. Now everything is fine. Regarding trjorder, it doesn't measure h-bonds but gives the water nearest to protein. I wouldn't try to draw any sort of comparison between the output of trjorder and g_hbond. If you want to measure H-bonds, there's only one tool for that. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/Search before posting! * Please don'
Re: [gmx-users] Re: g_analyze
Hi, I tried g_select to dump the structure with the interacting water molecules, but I don't know know how to do that. I searched for some threads in the discussion but wasn't able to find anything related to my need. Can you explain how can I do that ? On Tue, Nov 12, 2013 at 7:39 AM, bharat gupta wrote: > Sorry, I attached the wrong file . Here's the average file generate from > one of the files I sent in my last mail. I used the command g_analyze -f > hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file obtained > from this command :- > > https://www.dropbox.com/s/sovzk40cudznfjw/hbond_115-water-avg.xvg > > Now, if you see, the graph (in previous mail) and average file, both > correlates well. I have a doubt about interpreting the result from > g_analyze. The value "7.150740e+00" implies that on average 7 hydrogen > bonds are formed during the simulation time of 5ns to 10ns. What does then > the average file or its graph tells ?? > > > > On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul wrote: > >> >> >> On 11/11/13 4:06 AM, bharat gupta wrote: >> >>> In addition to my previous question, I have another question about >>> g_analyze. When I used the hbond.xvg file to get the average and plotted >>> the average.xvg file I found that the average value is round 4 to 5 >>> according to the graph. But g_analyze in its final calculation gives >>> 7.150 >>> as the average values... Here's the link for the graph and result of >>> average value calculated by g_analyze :- >>> >>>std. dev.relative deviation of >>> standard - cumulants from those >>> of >>> set average deviation sqrt(n-1) a Gaussian distribition >>>cum. 3 cum. 4 >>> SS1 * 7.150740e+00 * 8.803173e-01 1.760635e-02 0.0620.163 >>> >>> SS2 1.490604e+00 1.164761e+00 2.329523e-02 0.4950.153 >>> >>> https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png >>> >>> Here's the link hbond.xvg file and its averaged file >>> https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg >>> https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg >>> >>> >> Neither of these files produce output that corresponds to the PNG image >> above. Both files have values in 6-9 H-bond range and thus agree with the >> g_analyze output, which I can reproduce. I suspect you're somehow getting >> your files mixed up. >> >> >> -Justin >> >> >>> On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta >>> wrote: >>> >>> thank you informing about g_rdf... Is it possible to dump the structure with those average water molecules interacting with the residues. I generated the hbond.log file which gives the details but I need to generate a figure for this ?? On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul wrote: > > On 11/10/13 8:38 PM, bharat gupta wrote: > > But trjorder can be used to calculate the hydration layer or shell >> around >> residues ... Right ?? >> >> >> Yes, but I also tend to think that integrating an RDF is also a more > straightforward way of doing that. With trjorder, you set some > arbitrary > cutoff that may or may not be an informed decision - with an RDF it is > clear where the hydration layers are. > > -Justin > > > > On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul >> wrote: >> >> >> >>> On 11/10/13 8:30 PM, bharat gupta wrote: >>> >>> Thanks for your reply. I was missing the scientific notation part. >>> Now >>> everything is fine. Regarding trjorder, it doesn't measure h-bonds but gives the water nearest to protein. I wouldn't try to draw any sort of comparison between the output of >>> trjorder and g_hbond. If you want to measure H-bonds, there's only >>> one >>> tool for that. >>> >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 601 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> >>> == >>> -- >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> * 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-requ...@gromacs.org. >>> * Can't
Re: [gmx-users] Re: g_analyze
Sorry, I attached the wrong file . Here's the average file generate from one of the files I sent in my last mail. I used the command g_analyze -f hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file obtained from this command :- https://www.dropbox.com/s/sovzk40cudznfjw/hbond_115-water-avg.xvg Now, if you see, the graph (in previous mail) and average file, both correlates well. I have a doubt about interpreting the result from g_analyze. The value "7.150740e+00" implies that on average 7 hydrogen bonds are formed during the simulation time of 5ns to 10ns. What does then the average file or its graph tells ?? On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul wrote: > > > On 11/11/13 4:06 AM, bharat gupta wrote: > >> In addition to my previous question, I have another question about >> g_analyze. When I used the hbond.xvg file to get the average and plotted >> the average.xvg file I found that the average value is round 4 to 5 >> according to the graph. But g_analyze in its final calculation gives 7.150 >> as the average values... Here's the link for the graph and result of >> average value calculated by g_analyze :- >> >>std. dev.relative deviation of >> standard - cumulants from those of >> set average deviation sqrt(n-1) a Gaussian distribition >>cum. 3 cum. 4 >> SS1 * 7.150740e+00 * 8.803173e-01 1.760635e-02 0.0620.163 >> >> SS2 1.490604e+00 1.164761e+00 2.329523e-02 0.4950.153 >> >> https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png >> >> Here's the link hbond.xvg file and its averaged file >> https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg >> https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg >> >> > Neither of these files produce output that corresponds to the PNG image > above. Both files have values in 6-9 H-bond range and thus agree with the > g_analyze output, which I can reproduce. I suspect you're somehow getting > your files mixed up. > > > -Justin > > >> On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta >> wrote: >> >> thank you informing about g_rdf... >>> >>> Is it possible to dump the structure with those average water molecules >>> interacting with the residues. I generated the hbond.log file which gives >>> the details but I need to generate a figure for this ?? >>> >>> >>> >>> On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul wrote: >>> >>> On 11/10/13 8:38 PM, bharat gupta wrote: But trjorder can be used to calculate the hydration layer or shell > around > residues ... Right ?? > > > Yes, but I also tend to think that integrating an RDF is also a more straightforward way of doing that. With trjorder, you set some arbitrary cutoff that may or may not be an informed decision - with an RDF it is clear where the hydration layers are. -Justin On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul > wrote: > > > >> On 11/10/13 8:30 PM, bharat gupta wrote: >> >> Thanks for your reply. I was missing the scientific notation part. >> Now >> >>> everything is fine. >>> >>> Regarding trjorder, it doesn't measure h-bonds but gives the water >>> nearest >>> to protein. >>> >>> >>> I wouldn't try to draw any sort of comparison between the output of >>> >> trjorder and g_hbond. If you want to measure H-bonds, there's only >> one >> tool for that. >> >> >> -Justin >> >> -- >> == >> >> Justin A. Lemkul, Ph.D. >> Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 601 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> >> == >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * 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-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441
Re: [gmx-users] Re: g_analyze
On 11/11/13 4:06 AM, bharat gupta wrote: In addition to my previous question, I have another question about g_analyze. When I used the hbond.xvg file to get the average and plotted the average.xvg file I found that the average value is round 4 to 5 according to the graph. But g_analyze in its final calculation gives 7.150 as the average values... Here's the link for the graph and result of average value calculated by g_analyze :- std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 * 7.150740e+00 * 8.803173e-01 1.760635e-02 0.0620.163 SS2 1.490604e+00 1.164761e+00 2.329523e-02 0.4950.153 https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png Here's the link hbond.xvg file and its averaged file https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg Neither of these files produce output that corresponds to the PNG image above. Both files have values in 6-9 H-bond range and thus agree with the g_analyze output, which I can reproduce. I suspect you're somehow getting your files mixed up. -Justin On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta wrote: thank you informing about g_rdf... Is it possible to dump the structure with those average water molecules interacting with the residues. I generated the hbond.log file which gives the details but I need to generate a figure for this ?? On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul wrote: On 11/10/13 8:38 PM, bharat gupta wrote: But trjorder can be used to calculate the hydration layer or shell around residues ... Right ?? Yes, but I also tend to think that integrating an RDF is also a more straightforward way of doing that. With trjorder, you set some arbitrary cutoff that may or may not be an informed decision - with an RDF it is clear where the hydration layers are. -Justin On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul wrote: On 11/10/13 8:30 PM, bharat gupta wrote: Thanks for your reply. I was missing the scientific notation part. Now everything is fine. Regarding trjorder, it doesn't measure h-bonds but gives the water nearest to protein. I wouldn't try to draw any sort of comparison between the output of trjorder and g_hbond. If you want to measure H-bonds, there's only one tool for that. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_analyze
On 11/11/13 1:30 AM, bharat gupta wrote: thank you informing about g_rdf... Is it possible to dump the structure with those average water molecules interacting with the residues. I generated the hbond.log file which gives the details but I need to generate a figure for this ?? g_select -Justin On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul wrote: On 11/10/13 8:38 PM, bharat gupta wrote: But trjorder can be used to calculate the hydration layer or shell around residues ... Right ?? Yes, but I also tend to think that integrating an RDF is also a more straightforward way of doing that. With trjorder, you set some arbitrary cutoff that may or may not be an informed decision - with an RDF it is clear where the hydration layers are. -Justin On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul wrote: On 11/10/13 8:30 PM, bharat gupta wrote: Thanks for your reply. I was missing the scientific notation part. Now everything is fine. Regarding trjorder, it doesn't measure h-bonds but gives the water nearest to protein. I wouldn't try to draw any sort of comparison between the output of trjorder and g_hbond. If you want to measure H-bonds, there's only one tool for that. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_analyze
In addition to my previous question, I have another question about g_analyze. When I used the hbond.xvg file to get the average and plotted the average.xvg file I found that the average value is round 4 to 5 according to the graph. But g_analyze in its final calculation gives 7.150 as the average values... Here's the link for the graph and result of average value calculated by g_analyze :- std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 * 7.150740e+00 * 8.803173e-01 1.760635e-02 0.0620.163 SS2 1.490604e+00 1.164761e+00 2.329523e-02 0.4950.153 https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png Here's the link hbond.xvg file and its averaged file https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta wrote: > thank you informing about g_rdf... > > Is it possible to dump the structure with those average water molecules > interacting with the residues. I generated the hbond.log file which gives > the details but I need to generate a figure for this ?? > > > > On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul wrote: > >> >> >> On 11/10/13 8:38 PM, bharat gupta wrote: >> >>> But trjorder can be used to calculate the hydration layer or shell around >>> residues ... Right ?? >>> >>> >> Yes, but I also tend to think that integrating an RDF is also a more >> straightforward way of doing that. With trjorder, you set some arbitrary >> cutoff that may or may not be an informed decision - with an RDF it is >> clear where the hydration layers are. >> >> -Justin >> >> >> >>> On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul wrote: >>> >>> On 11/10/13 8:30 PM, bharat gupta wrote: Thanks for your reply. I was missing the scientific notation part. Now > everything is fine. > > Regarding trjorder, it doesn't measure h-bonds but gives the water > nearest > to protein. > > > I wouldn't try to draw any sort of comparison between the output of trjorder and g_hbond. If you want to measure H-bonds, there's only one tool for that. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> -- >> == >> >> Justin A. Lemkul, Ph.D. >> Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 601 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> >> == >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * 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-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_analyze
thank you informing about g_rdf... Is it possible to dump the structure with those average water molecules interacting with the residues. I generated the hbond.log file which gives the details but I need to generate a figure for this ?? On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul wrote: > > > On 11/10/13 8:38 PM, bharat gupta wrote: > >> But trjorder can be used to calculate the hydration layer or shell around >> residues ... Right ?? >> >> > Yes, but I also tend to think that integrating an RDF is also a more > straightforward way of doing that. With trjorder, you set some arbitrary > cutoff that may or may not be an informed decision - with an RDF it is > clear where the hydration layers are. > > -Justin > > > >> On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul wrote: >> >> >>> >>> On 11/10/13 8:30 PM, bharat gupta wrote: >>> >>> Thanks for your reply. I was missing the scientific notation part. Now everything is fine. Regarding trjorder, it doesn't measure h-bonds but gives the water nearest to protein. I wouldn't try to draw any sort of comparison between the output of >>> trjorder and g_hbond. If you want to measure H-bonds, there's only one >>> tool for that. >>> >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 601 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> >>> == >>> -- >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> * 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-requ...@gromacs.org. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * 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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_analyze
On 11/10/13 8:38 PM, bharat gupta wrote: But trjorder can be used to calculate the hydration layer or shell around residues ... Right ?? Yes, but I also tend to think that integrating an RDF is also a more straightforward way of doing that. With trjorder, you set some arbitrary cutoff that may or may not be an informed decision - with an RDF it is clear where the hydration layers are. -Justin On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul wrote: On 11/10/13 8:30 PM, bharat gupta wrote: Thanks for your reply. I was missing the scientific notation part. Now everything is fine. Regarding trjorder, it doesn't measure h-bonds but gives the water nearest to protein. I wouldn't try to draw any sort of comparison between the output of trjorder and g_hbond. If you want to measure H-bonds, there's only one tool for that. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_analyze
But trjorder can be used to calculate the hydration layer or shell around residues ... Right ?? On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul wrote: > > > On 11/10/13 8:30 PM, bharat gupta wrote: > >> Thanks for your reply. I was missing the scientific notation part. Now >> everything is fine. >> >> Regarding trjorder, it doesn't measure h-bonds but gives the water nearest >> to protein. >> >> > I wouldn't try to draw any sort of comparison between the output of > trjorder and g_hbond. If you want to measure H-bonds, there's only one > tool for that. > > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * 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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_analyze
On 11/10/13 8:30 PM, bharat gupta wrote: Thanks for your reply. I was missing the scientific notation part. Now everything is fine. Regarding trjorder, it doesn't measure h-bonds but gives the water nearest to protein. I wouldn't try to draw any sort of comparison between the output of trjorder and g_hbond. If you want to measure H-bonds, there's only one tool for that. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_analyze
Thanks for your reply. I was missing the scientific notation part. Now everything is fine. Regarding trjorder, it doesn't measure h-bonds but gives the water nearest to protein. On Mon, Nov 11, 2013 at 10:12 AM, Justin Lemkul wrote: > > > On 11/10/13 7:18 PM, bharat gupta wrote: > >> I checked the file hbnum.xvg file and it contains three columns - time, >> hbonds, hbonds that donot follow the angle criteria. In that case SS1 is >> > > The third column is not actually H-bonds, then ;) > > > the average of actual hbonds (2nd column ) and SS2 is the average of 3rd >> column. Am I right here or not ?? >> >> > Yes. > > > I tried to calculate the h-bond for residues 115-118 individually, and >> then >> checked the average for each residue. For single residue calculation, the >> g_analyze average value is correct. >> >> But when I calculate the h-bond as a range 115-118, I get the g_analyze >> value as 1.62 . I calculated the average manually in excel, got the >> average >> values as 16.2 [which is (g_analyze avg value)/10]. >> >> > That is impossible. You cannot get a different average by examining the > same numbers. Read the g_analyze output again - I am willing to bet that > you're not seeing the exponent of the scientific notation. > > > I then added up the average values of h-bonds of individual residues and >> the final comes around 16.2, same as that of the 115-118 range h-bonds. >> This means that my calculation is correct. >> >> I also used trjorder to calculate h-bond at distance 0.34 for residues >> 115-118. I got the average value around 2.51 from g_analyze, where as >> manual calculation gives 25.1. I don't knw why for the range the g_analyze >> give avg as (actual avg value)/10 ?? >> >> Why does trjorder and g_hbond gives different number of hydrogen bonds for >> the same residue set?? >> >> > All of this comes down to correctly reading the screen output. I have no > idea what you're doing with trjorder, though. It doesn't measure H-bonds. > > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * 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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_analyze
On 11/10/13 7:18 PM, bharat gupta wrote: I checked the file hbnum.xvg file and it contains three columns - time, hbonds, hbonds that donot follow the angle criteria. In that case SS1 is The third column is not actually H-bonds, then ;) the average of actual hbonds (2nd column ) and SS2 is the average of 3rd column. Am I right here or not ?? Yes. I tried to calculate the h-bond for residues 115-118 individually, and then checked the average for each residue. For single residue calculation, the g_analyze average value is correct. But when I calculate the h-bond as a range 115-118, I get the g_analyze value as 1.62 . I calculated the average manually in excel, got the average values as 16.2 [which is (g_analyze avg value)/10]. That is impossible. You cannot get a different average by examining the same numbers. Read the g_analyze output again - I am willing to bet that you're not seeing the exponent of the scientific notation. I then added up the average values of h-bonds of individual residues and the final comes around 16.2, same as that of the 115-118 range h-bonds. This means that my calculation is correct. I also used trjorder to calculate h-bond at distance 0.34 for residues 115-118. I got the average value around 2.51 from g_analyze, where as manual calculation gives 25.1. I don't knw why for the range the g_analyze give avg as (actual avg value)/10 ?? Why does trjorder and g_hbond gives different number of hydrogen bonds for the same residue set?? All of this comes down to correctly reading the screen output. I have no idea what you're doing with trjorder, though. It doesn't measure H-bonds. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_analyze
I checked the file hbnum.xvg file and it contains three columns - time, hbonds, hbonds that donot follow the angle criteria. In that case SS1 is the average of actual hbonds (2nd column ) and SS2 is the average of 3rd column. Am I right here or not ?? I tried to calculate the h-bond for residues 115-118 individually, and then checked the average for each residue. For single residue calculation, the g_analyze average value is correct. But when I calculate the h-bond as a range 115-118, I get the g_analyze value as 1.62 . I calculated the average manually in excel, got the average values as 16.2 [which is (g_analyze avg value)/10]. I then added up the average values of h-bonds of individual residues and the final comes around 16.2, same as that of the 115-118 range h-bonds. This means that my calculation is correct. I also used trjorder to calculate h-bond at distance 0.34 for residues 115-118. I got the average value around 2.51 from g_analyze, where as manual calculation gives 25.1. I don't knw why for the range the g_analyze give avg as (actual avg value)/10 ?? Why does trjorder and g_hbond gives different number of hydrogen bonds for the same residue set?? Thanks --- BHARAT On Sun, Nov 10, 2013 at 10:01 PM, Justin Lemkul wrote: > > > On 11/10/13 12:20 AM, bharat gupta wrote: > >> Hi, >> I used the command g_hbond to find h-bond between residues 115-118 and >> water. Then I used g_analyze to find out the average and it gives the >> value >> for the hbonds like this :- >> >>std. dev.relative deviation of >> standard - cumulants from those of >> set average deviation sqrt(n-1) a Gaussian distribition >>cum. 3 cum. 4 >> SS1 6.877249e-02 2.546419e-01 5.092839e-03 2.1813.495 >> SS2 6.997201e-02 2.673450e-01 5.346901e-03 2.4215.001 >> >> When I calculated the average manually, by taking the average of numbers >> in >> second column of hbnum.xvg file, I got a value of around 13.5.. What is >> the >> reason for such a large difference. >> >> > Hard to say, but I've never known g_analyze to be wrong, so I'd suspect > something is amiss in your manual calculation. The difference between 13.5 > and 0.0069 is huge; you should be able to scan through the data file to see > what the expected value should be. > > > In another case, g_analyze gives avg values of aroun 6.9 for hbond between >> two residues and when I calculated it maually I got the avg values as 6.8 >> >>> .. >>> >> >> Whats the meaning of SS1 and SS2,?? Does it mean that SS1 refers to time >> and SS2 refers to hbond numbers in the hbnum.xvg obtained from g_hbond >> analysis ?? >> > > Data sets 1 and 2. You will note that there are two columns of data in > the -hbnum output produced by g_hbond, with titles explaining both. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * 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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_analyze
On 11/10/13 12:20 AM, bharat gupta wrote: Hi, I used the command g_hbond to find h-bond between residues 115-118 and water. Then I used g_analyze to find out the average and it gives the value for the hbonds like this :- std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 6.877249e-02 2.546419e-01 5.092839e-03 2.1813.495 SS2 6.997201e-02 2.673450e-01 5.346901e-03 2.4215.001 When I calculated the average manually, by taking the average of numbers in second column of hbnum.xvg file, I got a value of around 13.5.. What is the reason for such a large difference. Hard to say, but I've never known g_analyze to be wrong, so I'd suspect something is amiss in your manual calculation. The difference between 13.5 and 0.0069 is huge; you should be able to scan through the data file to see what the expected value should be. In another case, g_analyze gives avg values of aroun 6.9 for hbond between two residues and when I calculated it maually I got the avg values as 6.8 .. Whats the meaning of SS1 and SS2,?? Does it mean that SS1 refers to time and SS2 refers to hbond numbers in the hbnum.xvg obtained from g_hbond analysis ?? Data sets 1 and 2. You will note that there are two columns of data in the -hbnum output produced by g_hbond, with titles explaining both. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: g_analyze
Hi, I used the command g_hbond to find h-bond between residues 115-118 and water. Then I used g_analyze to find out the average and it gives the value for the hbonds like this :- std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 6.877249e-02 2.546419e-01 5.092839e-03 2.1813.495 SS2 6.997201e-02 2.673450e-01 5.346901e-03 2.4215.001 When I calculated the average manually, by taking the average of numbers in second column of hbnum.xvg file, I got a value of around 13.5.. What is the reason for such a large difference. In another case, g_analyze gives avg values of aroun 6.9 for hbond between two residues and when I calculated it maually I got the avg values as 6.8 >.. Whats the meaning of SS1 and SS2,?? Does it mean that SS1 refers to time and SS2 refers to hbond numbers in the hbnum.xvg obtained from g_hbond analysis ?? Please clarify these doubts.. Regards Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
