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 <jalem...@vt.edu> 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 <bharat.85.m...@gmail.com> >> 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 <jalem...@vt.edu> 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 0.062 0.163 >>>>> >>>>> SS2 1.490604e+00 1.164761e+00 2.329523e-02 0.495 0.153 >>>>> >>>>> 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 <jalem...@vt.edu> >>>>>> 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 <jalem...@vt.edu> >>>>>>> >>>>>>>> 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 list gmx-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 list gmx-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 list gmx-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 list gmx-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? 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