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 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 0.0620.163 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 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 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
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 bharat.85.m...@gmail.comwrote: 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 0.0620.163 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 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 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
[gmx-users] installation error under openSuse 12.2
Date: Mon, 11 Nov 2013 08:27:05 -0800 (PST) From: kolnkempff kolnkem...@gmail.com Subject: [gmx-users] installation error under openSuse 12.2 To: gmx-users@gromacs.org Message-ID: 1384187225465-5012430.p...@n6.nabble.com Content-Type: text/plain; charset=us-ascii Dear gmx-users, I am trying to install gromacs-4.6.3 on an older Dell that is running openSuse 12.2 Using DGMX_BUILD_OWN_FFTW=ON failed for me so to get through cmake I had to compile fftw from scratch and I followed the recommendation of going directly to their website. Now I am at the make stage and get the following message: [ 67%] Built target gmxfftw make[2]: *** No rule to make target `//home/koln/bin/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3f.a', needed by `src/gmxlib/libgmx.so.8'. Stop. make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 make: *** [all] Error 2 When I check for libfftw, I get: koln@linux-5bim:~/bin/gromacs-4.6.3/build2 rpm -qf /usr/lib/libfftw3f.* libfftw3-3-32bit-3.3.2-1.1.2.x86_64 Any suggestions for how to get past this obstacle would be greatly appreciated! This is an known issue in OpenSuse! We added a workaround a while ago: https://gerrit.gromacs.org/#/c/2540/ Until Gromacs release 4.6.4. you will have to change line 41 of src/contrib/fftw/CMakeLists.txt yourself or just install fftw through OpenSuse or by hand. Christoph Koln -- View this message in context: http://gromacs.5086.x6.nabble.com/installation-error-under-openSuse-12-2-tp5012430.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Christoph Junghans Web: http://www.compphys.de -- 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: installation error under openSuse 12.2
Thank you so much Justin. On the one hand, I feel dumb because I could have sworn that I was using a clean build directory. On the other hand, I obviously lost track of what I was doing because your suggestion worked like a charm! Koln -- View this message in context: http://gromacs.5086.x6.nabble.com/installation-error-under-openSuse-12-2-tp5012430p5012436.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Calculating diffusion coefficient in three dimension
Dear all, I am simulating a spherical lipid vesicle. I want to calculate the diffusion coefficient for each lipid component in 3D. How to calculate it using g_msd (or any other tool like g_velacc)? Thank you for your concern -- With Best Wishes Venkat Reddy Chirasani -- 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] hydrogen bond calculation problem
On 11/11/13 12:36 PM, Sushma Yadav wrote: Dear gromacs users, I have NaCl-water system of finite concentration .I want to calculate water-water hydrogen bond in the first solvation shell around ion..So I used g_hbond -shell option.For single ion in water,its easy to calculate..But say,for water-water hydrogen bonds around two Na+ ions,it is saying to Select one atom for shell. Although I have more than 1 Na+ ions and I want to see water-water hydrogen bond around all Na+ ions simultaneously.Is it possible to take solvation shell of each ion at a same time? According to the help description for the -shell option, no. Only one particle can be considered at a time. You'll have to analyze each Na+ separately, which is easily scripted. -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] Restarting a simulation after replacing an empty md.trr file
Dear Gromacs users, I am running a 50ns simulation of a protein having nearly 700 residues on 60 threads (Gromacs 4.6.3). At one point i got a disk space problem, so i have deleted the md.trr file and created an empty md.trr file. when i tried to restart the simulation from check point file on 100 threads, [ mdrun -v -deffnm md -cpi md.cpt -nt 100 ] i am getting a note and an error as fallows Reading checkpoint file md.cpt generated: #PME-nodes mismatch, current program: 100 checkpoint file: 60 Gromacs binary or parallel settings not identical to previous run. Continuation is exact, but is not guaranteed to be binary identical. ... Source code file: checkpoint.c, line: 1767 Fatal error: Can't read 1048576 bytes of 'md.trr' to compute checksum. The file has been replaced or its contents has been modified. please help me in overcoming this problem. Thanking you. -- Arun Kumar Somavarapu Project-JRF Dr. Pawan Gupta's lab Protein Science and Engineering Dept, Institute of Microbial Tecnology, Sec 39-A, Chandigarh - 160036. -- 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: Reaction field zero and ions
On 11/11/13 12:08 PM, Williams Ernesto Miranda Delgado wrote: Hello If I did the MD simulation using PME and neutralized with ions, and I want to rerun this time with reaction field zero, is there any problem if I keep the ions? This is for LIE calculation. I am using AMBER99SB. Why do you think it necessary to delete them? -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] Calculating diffusion coefficient in three dimension
MSD is 3D by default. Dr. Vitaly V. Chaban On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy venkat...@gmail.com wrote: Dear all, I am simulating a spherical lipid vesicle. I want to calculate the diffusion coefficient for each lipid component in 3D. How to calculate it using g_msd (or any other tool like g_velacc)? Thank you for your concern -- With Best Wishes Venkat Reddy Chirasani -- 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: Reaction field zero and ions
There are no problems to have ions while using Reaction-Field treatment. Dr. Vitaly V. Chaban On Mon, Nov 11, 2013 at 7:06 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/11/13 12:08 PM, Williams Ernesto Miranda Delgado wrote: Hello If I did the MD simulation using PME and neutralized with ions, and I want to rerun this time with reaction field zero, is there any problem if I keep the ions? This is for LIE calculation. I am using AMBER99SB. Why do you think it necessary to delete them? -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 11/11/13 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 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 0.0620.163 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 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 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
Re: [gmx-users] Restarting a simulation after replacing an empty md.trr file
On 11/12/13 1:15 AM, arun kumar wrote: Dear Gromacs users, I am running a 50ns simulation of a protein having nearly 700 residues on 60 threads (Gromacs 4.6.3). At one point i got a disk space problem, so i have deleted the md.trr file and created an empty md.trr file. when i tried to restart the simulation from check point file on 100 threads, [ mdrun -v -deffnm md -cpi md.cpt -nt 100 ] i am getting a note and an error as fallows Reading checkpoint file md.cpt generated: #PME-nodes mismatch, current program: 100 checkpoint file: 60 Gromacs binary or parallel settings not identical to previous run. Continuation is exact, but is not guaranteed to be binary identical. ... Source code file: checkpoint.c, line: 1767 Fatal error: Can't read 1048576 bytes of 'md.trr' to compute checksum. The file has been replaced or its contents has been modified. please help me in overcoming this problem. Use -noappend. If you mess with any of the files that mdrun produces, the file appending procedure (which is the default behavior) will fail. -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
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.comwrote: 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 0.0620.163 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 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 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
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 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 0.0620.163 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 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 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
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 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 0.0620.163 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 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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users *
Re: [gmx-users] Calculating diffusion coefficient in three dimension
Thank you sir for the prompt reply. *g_msd -f traj.xtc -s topol.tpr -n msd.ndx -lateral z -o msd.xvg -tu ns* Here I am giving -lateral z (like for membrane simulations). Is it fine for spherical systems also? On Tue, Nov 12, 2013 at 5:32 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: MSD is 3D by default. Dr. Vitaly V. Chaban On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy venkat...@gmail.com wrote: Dear all, I am simulating a spherical lipid vesicle. I want to calculate the diffusion coefficient for each lipid component in 3D. How to calculate it using g_msd (or any other tool like g_velacc)? Thank you for your concern -- With Best Wishes Venkat Reddy Chirasani -- 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 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] Calculating diffusion coefficient in three dimension
On 11/12/13 8:55 AM, Venkat Reddy wrote: Thank you sir for the prompt reply. *g_msd -f traj.xtc -s topol.tpr -n msd.ndx -lateral z -o msd.xvg -tu ns* Here I am giving -lateral z (like for membrane simulations). Is it fine for spherical systems also? No. The system is a sphere, so what use is it to calculate motion perpendicular to z when you have lipids moving in all three spatial dimensions? A vesicle is very different from a membrane, in which the lipids move in a plane, thus making -lateral z useful. -Justin On Tue, Nov 12, 2013 at 5:32 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: MSD is 3D by default. Dr. Vitaly V. Chaban On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy venkat...@gmail.com wrote: Dear all, I am simulating a spherical lipid vesicle. I want to calculate the diffusion coefficient for each lipid component in 3D. How to calculate it using g_msd (or any other tool like g_velacc)? Thank you for your concern -- With Best Wishes Venkat Reddy Chirasani -- 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 -- == 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: ok, thank you
Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Restarting a simulation after replacing an empty md.trr file (arun kumar) 2. Re: Re: Reaction field zero and ions (Justin Lemkul) 3. Re: Calculating diffusion coefficient in three dimension (Dr. Vitaly Chaban) 4. Re: Re: Reaction field zero and ions (Dr. Vitaly Chaban) 5. Re: Re: g_analyze (Justin Lemkul) 6. Re: Re: g_analyze (Justin Lemkul) -- Message: 1 Date: Tue, 12 Nov 2013 11:45:05 +0530 From: arun kumar arunjones.kuma...@gmail.com Subject: [gmx-users] Restarting a simulation after replacing an empty md.trr file To: gmx-users@gromacs.org Message-ID: cagm9vj8dn+fqb-cigjdvv+i1mq7mc2cxvkde3gsp5+lwhds...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Dear Gromacs users, I am running a 50ns simulation of a protein having nearly 700 residues on 60 threads (Gromacs 4.6.3). At one point i got a disk space problem, so i have deleted the md.trr file and created an empty md.trr file. when i tried to restart the simulation from check point file on 100 threads, [ mdrun -v -deffnm md -cpi md.cpt -nt 100 ] i am getting a note and an error as fallows Reading checkpoint file md.cpt generated: #PME-nodes mismatch, current program: 100 checkpoint file: 60 Gromacs binary or parallel settings not identical to previous run. Continuation is exact, but is not guaranteed to be binary identical. ... Source code file: checkpoint.c, line: 1767 Fatal error: Can't read 1048576 bytes of 'md.trr' to compute checksum. The file has been replaced or its contents has been modified. please help me in overcoming this problem. Thanking you. -- Arun Kumar Somavarapu Project-JRF Dr. Pawan Gupta's lab Protein Science and Engineering Dept, Institute of Microbial Tecnology, Sec 39-A, Chandigarh - 160036. -- Message: 2 Date: Mon, 11 Nov 2013 13:06:32 -0500 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Re: Reaction field zero and ions To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 52811ca8.5030...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 11/11/13 12:08 PM, Williams Ernesto Miranda Delgado wrote: Hello If I did the MD simulation using PME and neutralized with ions, and I want to rerun this time with reaction field zero, is there any problem if I keep the ions? This is for LIE calculation. I am using AMBER99SB. Why do you think it necessary to delete them? -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 == -- Message: 3 Date: Tue, 12 Nov 2013 13:02:54 +0100 From: Dr. Vitaly Chaban vvcha...@gmail.com Subject: Re: [gmx-users] Calculating diffusion coefficient in three dimension To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: capxdd+abay6mj_dkn6_k+mkbuty4eyzspdvdxj+m-m-2zae...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 MSD is 3D by default. Dr. Vitaly V. Chaban On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy venkat...@gmail.com wrote: Dear all, I am simulating a spherical lipid vesicle. I want to calculate the diffusion coefficient for each lipid component in 3D. How to calculate it using g_msd (or any other tool like g_velacc)? Thank you for your concern -- With Best Wishes Venkat Reddy Chirasani -- 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 -- Message: 4 Date: Tue, 12 Nov 2013 13:04:10 +0100 From: Dr. Vitaly Chaban vvcha...@gmail.com Subject: Re: [gmx-users] Re: Reaction field zero and ions To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID:
[gmx-users] Invalid order for directive defaults
Dear all My system contains protein + cnt + water molecules. I have summarized what I did below: --- 1) By pdb2gmx and charmm27 force field, I obtained pr.top for protein then I converted it into pr.itp by deleting ; Include forcefield parameters #include charmm27.ff/forcefield.itp from begining of file and by deleting ; Include water topology #include charmm27.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include charmm27.ff/ions.itp [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_chain_A 1 from ending of file. 2) I used bonded and nonbonded parameters for cnt from paper: J. Phys. Chem. B 2001, 105, 9980-9987 (Carbon Nanotubes in Water: Structural Characteristics and Energetics). I created cnt.ff folder containing following files: ffcnt.atp / ffcnt.n2t / ffcnt.rtp / ffcntbon.itp / ffcntnonbon.itp / forcefield.itp Then, I put cnt.ff folder in GMXLIB directory. 3) By g_x2top and cnt.ff created in previous step, I obtained cnt.top for cnt then I converted it into cnt.itp by deleting ; Include forcefield parameters #include cnt.ff/forcefield.itp from begining of file and by deleting [ system ] ; Name CNT [ molecules ] ; Compound#mols CNT 1 from ending of file. 4) I combined cnt and protein to create one coordination file (system.gro). Order of molecules are as follows: 1) cnt 2) protein 3) water. 5) I wrote a topol.top file given below, ; Include forcefield parameters #include cnt.ff/forcefield.itp #include cnt.itp #include charmm27.ff/forcefield.itp #include pr.itp ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include charmm27.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include charmm27.ff/ions.itp [ system ] ; Name CNT/Protein/SOL [ molecules ] ; Compound#mols CNT 1 Protein 1 SOL 1359 When I used grompp -f minim.mdp -c system.gro -p topol.top -o minim.tpr, I encountered with following error: Fatal error: Syntax error - File forcefield.itp, line 11 Last line read: '[ defaults ]' Invalid order for directive defaults Content of forcefield.itp in cnt.ff directory is as follows: *** *CHARMM port writted by * *Par Bjelkmar, Per Larsson, Michel Cuendet, * *Berk Hess and Erik Lindahl. * * Correspondance: * *bjelk...@cbr.su.se or lind...@cbr.su.se * *** #define _FF_CNT [ defaults ] ; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ 12yes1.01.0 #include ffcntnonbon.itp #include ffcntbon.itp and Content of forcefield.itp in Charmm27.ff directory is as follows: *** *CHARMM port writted by * *Par Bjelkmar, Per Larsson, Michel Cuendet, * *Berk Hess and Erik Lindahl. * * Correspondance: * *bjelk...@cbr.su.se or lind...@cbr.su.se * *** #define _FF_CHARMM [ defaults ] ; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ 12yes1.01.0 #include ffnonbonded.itp #include ffbonded.itp #include gb.itp #include cmap.itp ; Nucleic acids nonbonded and bonded parameters #include ffnanonbonded.itp #include ffnabonded.itp In both of forcefield.itp files, line 11 is [ defaults ]. I changed name of forcefield.itp file in cnt.ff directory to cntff.itp, but there is same error, again. That is all what I exactly did. Is anything wrong or missing? How to solve this error? Any help will highly appreciated --
Re: mdrun on 8-core AMD + GTX TITAN (was: Re: [gmx-users] Re: Gromacs-4.6 on two Titans GPUs)
As Mark said, please share the *entire* log file. Among other important things, the result of PP-PME tuning is not included above. However, I suspect that in this case scaling is strongly affected or by the small size of the system you are simulating. -- Szilárd On Sun, Nov 10, 2013 at 5:28 AM, Dwey Kauffman mpi...@gmail.com wrote: Hi Szilard, Thank you very much for your suggestions. Actually, I was jumping to conclusions too early, as you mentioned AMD cluster, I assumed you must have 12-16-core Opteron CPUs. If you have an 8-core (desktop?) AMD CPU, than you may not need to run more than one rank per GPU. Yes, we do have independent clusters of AMD, AMD opteron, Intel Corei7. All nodes of three clusters are installed with (at least) 1 GPU card. I have run the same test on these three clusters. Let's focus on a basic scaling issue: One GPU v.s Two GPUs within the same node of 8-core AMD cpu. Using 1 GPU, we can have a performance of ~32 ns/day. Using two GPU, we gain not much more ( ~38.5 ns/day ). It is about ~20% more performance. However, this is not really true because in some tests, I also saw only 2-5% more, which really surprised me. As you can see, this test was made on the same node regardless of networking. Can the performance be improved say 50% more when 2 GPUs are used on a general task ? If yes, how ? Indeed, as Richard pointed out, I was asking for *full* logs, these summaries can't tell much, the table above the summary entitled R E A L C Y C L E A N D T I M E A C C O U N T I N G as well as other reported information across the log file is what I need to make an assessment of your simulations' performance. Please see below. However, in your case I suspect that the bottleneck is multi-threaded scaling on the AMD CPUs and you should probably decrease the number of threads per MPI rank and share GPUs between 2-4 ranks. After I test all three clusters, I found it may NOT be an issue of AMD cpus. Intel cpus has the SAME scaling issue. However, I am curious as to how you justify the setup of 2-4 ranks sharing GPUs ? Can you please explain it a bit more ? You could try running mpirun -np 4 mdrun -ntomp 2 -gpu_id 0011 but I suspect this won't help because your scaling issue Your guess is correct but why is that ? it is worse. The more nodes are involved in a task, the performance is worse. in my experience even reaction field runs don't scale across nodes with 10G ethernet if you have more than 4-6 ranks per node trying to communicate (let alone with PME). What dose it mean let alone with PME ? how to do so ? by mdrun ? I do know mdrun -npme to specify PME process. Thank you. Dwey ### One GPU R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Th. Count Wall t (s) G-Cycles % - Neighbor search18 11 431.81713863.390 1.6 Launch GPU ops.18501 472.90615182.556 1.7 Force 185011328.61142654.785 4.9 PME mesh 18501 11561.327 371174.09042.8 Wait GPU local 185016888.008 221138.11125.5 NB X/F buffer ops. 189911216.49939055.455 4.5 Write traj.18 1030 12.741 409.039 0.0 Update 185011696.35854461.226 6.3 Constraints185011969.72663237.647 7.3 Rest 11458.82046835.133 5.4 - Total 1 27036.812 868011.431 100.0 - - PME spread/gather 18 10026975.086 223933.73925.8 PME 3D-FFT 18 10023928.259 126115.97614.5 PME solve 18501 636.48820434.327 2.4 - GPU timings - Computing: Count Wall t (s) ms/step % - Pair list H2D 11 43.4350.434 0.2 X / q H2D501 567.1680.113 2.8 Nonbonded F kernel 400 14174.3163.54470.8 Nonbonded F+ene k.904314.4384.79421.5 Nonbonded F+ene+prune k. 11 572.3705.724 2.9 F D2H
Re: [gmx-users] Invalid order for directive defaults
On 11/12/13 10:07 AM, Atila Petrosian wrote: Dear all My system contains protein + cnt + water molecules. I have summarized what I did below: --- 1) By pdb2gmx and charmm27 force field, I obtained pr.top for protein then I converted it into pr.itp by deleting ; Include forcefield parameters #include charmm27.ff/forcefield.itp from begining of file and by deleting ; Include water topology #include charmm27.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include charmm27.ff/ions.itp [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_chain_A 1 from ending of file. 2) I used bonded and nonbonded parameters for cnt from paper: J. Phys. Chem. B 2001, 105, 9980-9987 (Carbon Nanotubes in Water: Structural Characteristics and Energetics). I created cnt.ff folder containing following files: ffcnt.atp / ffcnt.n2t / ffcnt.rtp / ffcntbon.itp / ffcntnonbon.itp / forcefield.itp Then, I put cnt.ff folder in GMXLIB directory. 3) By g_x2top and cnt.ff created in previous step, I obtained cnt.top for cnt then I converted it into cnt.itp by deleting ; Include forcefield parameters #include cnt.ff/forcefield.itp from begining of file and by deleting [ system ] ; Name CNT [ molecules ] ; Compound#mols CNT 1 from ending of file. 4) I combined cnt and protein to create one coordination file (system.gro). Order of molecules are as follows: 1) cnt 2) protein 3) water. 5) I wrote a topol.top file given below, ; Include forcefield parameters #include cnt.ff/forcefield.itp #include cnt.itp #include charmm27.ff/forcefield.itp #include pr.itp ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include charmm27.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include charmm27.ff/ions.itp [ system ] ; Name CNT/Protein/SOL [ molecules ] ; Compound#mols CNT 1 Protein 1 SOL 1359 When I used grompp -f minim.mdp -c system.gro -p topol.top -o minim.tpr, I encountered with following error: Fatal error: Syntax error - File forcefield.itp, line 11 Last line read: '[ defaults ]' Invalid order for directive defaults Content of forcefield.itp in cnt.ff directory is as follows: *** *CHARMM port writted by * *Par Bjelkmar, Per Larsson, Michel Cuendet, * *Berk Hess and Erik Lindahl. * * Correspondance: * *bjelk...@cbr.su.se or lind...@cbr.su.se * *** #define _FF_CNT [ defaults ] ; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ 12yes1.01.0 #include ffcntnonbon.itp #include ffcntbon.itp and Content of forcefield.itp in Charmm27.ff directory is as follows: *** *CHARMM port writted by * *Par Bjelkmar, Per Larsson, Michel Cuendet, * *Berk Hess and Erik Lindahl. * * Correspondance: * *bjelk...@cbr.su.se or lind...@cbr.su.se * *** #define _FF_CHARMM [ defaults ] ; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ 12yes1.01.0 #include ffnonbonded.itp #include ffbonded.itp #include gb.itp #include cmap.itp ; Nucleic acids nonbonded and bonded parameters #include ffnanonbonded.itp #include ffnabonded.itp In both of forcefield.itp files, line 11 is [ defaults ]. I changed name of forcefield.itp file in cnt.ff directory to cntff.itp, but there is same error, again. That is all what I exactly did. Is anything wrong or missing? How to
[gmx-users] Re: segmentation fault on gromacs 4.5.5 after mdrun
I run grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr and everything looks fine. I check the nvt.tpr, and temperature is ok. the real problem is with the mdrun function. could be a problem of the software? Thanks Javier Justin Lemkul wrote On 11/11/13 11:24 AM, Carlos Javier Almeciga Diaz wrote: Hello evryone, I doing a simulation of a ligand-protein interaction with gromacs 4.5.5. Everything looks fine after I equilibrate the protein-ligand complex. I'm running these commands: grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr mdrun -deffnm nvt Nevertheless, I got this error: Reading file nvt.tpr, VERSION 4.5.5 (double precision) Segmentation fault What should I do? Instantaneous failure typically indicates that the forces are nonsensically high and the constraint algorithm immediately fails. Likely the previous energy minimization did not adequately complete. -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 jalemkul@.umaryland | (410) 706-7441 == -- gmx-users mailing list gmx-users@ 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-request@ . * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- View this message in context: http://gromacs.5086.x6.nabble.com/segmentation-fault-on-gromacs-4-5-5-after-mdrun-tp5012431p5012458.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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: Restarting a simulation after replacing an empty md.trr file
Hello Sir, Thanks for the reply. now is it fine if i use 100 threads in my restart. is there any impact on the over all simulation? -- View this message in context: http://gromacs.5086.x6.nabble.com/Restarting-a-simulation-after-replacing-an-empty-md-trr-file-tp5012443p5012459.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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: segmentation fault on gromacs 4.5.5 after mdrun
On 11/12/13 10:58 AM, cjalmeciga wrote: I run grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr and everything looks fine. I check the nvt.tpr, and temperature is ok. The fact that grompp completes indicates there is nothing syntactically wrong with the input files. Whether or not the content of the .mdp is physically sensible or the input configuration is plausible is an entirely different matter. Please tell us what the exact outcome of the previous energy minimization was (potential energy, maximum force, copied and pasted from screen output or .log file). the real problem is with the mdrun function. could be a problem of the software? You have presented no evidence that would lead anyone to believe the problem is with mdrun. In the vast majority of cases, user input is the problem. -Justin Thanks Javier Justin Lemkul wrote On 11/11/13 11:24 AM, Carlos Javier Almeciga Diaz wrote: Hello evryone, I doing a simulation of a ligand-protein interaction with gromacs 4.5.5. Everything looks fine after I equilibrate the protein-ligand complex. I'm running these commands: grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr mdrun -deffnm nvt Nevertheless, I got this error: Reading file nvt.tpr, VERSION 4.5.5 (double precision) Segmentation fault What should I do? Instantaneous failure typically indicates that the forces are nonsensically high and the constraint algorithm immediately fails. Likely the previous energy minimization did not adequately complete. -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 jalemkul@.umaryland | (410) 706-7441 == -- gmx-users mailing list gmx-users@ 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-request@ . * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- View this message in context: http://gromacs.5086.x6.nabble.com/segmentation-fault-on-gromacs-4-5-5-after-mdrun-tp5012431p5012458.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- == 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: Restarting a simulation after replacing an empty md.trr file
On 11/12/13 11:10 AM, arunjones wrote: Hello Sir, Thanks for the reply. now is it fine if i use 100 threads in my restart. is there any impact on the over all simulation? Only if that is the number of threads originally used in the run. If not, there will be a mismatch between the DD grid setup, the .cpt file will complain, and the run will fail. Rule of thumb: don't change settings or alter files mid-run ;) -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] Calculating diffusion coefficient in three dimension
Then, how to mention the direction for spherical particles Sir? On Tue, Nov 12, 2013 at 7:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 8:55 AM, Venkat Reddy wrote: Thank you sir for the prompt reply. *g_msd -f traj.xtc -s topol.tpr -n msd.ndx -lateral z -o msd.xvg -tu ns* Here I am giving -lateral z (like for membrane simulations). Is it fine for spherical systems also? No. The system is a sphere, so what use is it to calculate motion perpendicular to z when you have lipids moving in all three spatial dimensions? A vesicle is very different from a membrane, in which the lipids move in a plane, thus making -lateral z useful. -Justin On Tue, Nov 12, 2013 at 5:32 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: MSD is 3D by default. Dr. Vitaly V. Chaban On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy venkat...@gmail.com wrote: Dear all, I am simulating a spherical lipid vesicle. I want to calculate the diffusion coefficient for each lipid component in 3D. How to calculate it using g_msd (or any other tool like g_velacc)? Thank you for your concern -- With Best Wishes Venkat Reddy Chirasani -- 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 -- == 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 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] Calculating diffusion coefficient in three dimension
On 11/12/13 11:25 AM, Venkat Reddy wrote: Then, how to mention the direction for spherical particles Sir? Read g_msd -h again, paying specific attention to the -type flag. -Justin On Tue, Nov 12, 2013 at 7:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 8:55 AM, Venkat Reddy wrote: Thank you sir for the prompt reply. *g_msd -f traj.xtc -s topol.tpr -n msd.ndx -lateral z -o msd.xvg -tu ns* Here I am giving -lateral z (like for membrane simulations). Is it fine for spherical systems also? No. The system is a sphere, so what use is it to calculate motion perpendicular to z when you have lipids moving in all three spatial dimensions? A vesicle is very different from a membrane, in which the lipids move in a plane, thus making -lateral z useful. -Justin On Tue, Nov 12, 2013 at 5:32 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: MSD is 3D by default. Dr. Vitaly V. Chaban On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy venkat...@gmail.com wrote: Dear all, I am simulating a spherical lipid vesicle. I want to calculate the diffusion coefficient for each lipid component in 3D. How to calculate it using g_msd (or any other tool like g_velacc)? Thank you for your concern -- With Best Wishes Venkat Reddy Chirasani -- 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 -- == 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] Re: Restarting a simulation after replacing an empty md.trr file
Thank you Sir, initially i was running on 60 threads, now i changed it to 100. simulation is running with out any error, but i found a note in the log file as fallows #nodes mismatch, current program: 100 checkpoint file: 60 #PME-nodes mismatch, current program: -1 checkpoint file: 12 Gromacs binary or parallel settings not identical to previous run. Continuation is exact, but is not guaranteed to be binary identical. Initializing Domain Decomposition on 100 nodes is it a good idea to continue or shall i stick with 60 threads. -- View this message in context: http://gromacs.5086.x6.nabble.com/Restarting-a-simulation-after-replacing-an-empty-md-trr-file-tp5012443p5012463.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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: Restarting a simulation after replacing an empty md.trr file
On 11/12/13 12:07 PM, arunjones wrote: Thank you Sir, initially i was running on 60 threads, now i changed it to 100. simulation is running with out any error, but i found a note in the log file as fallows #nodes mismatch, current program: 100 checkpoint file: 60 #PME-nodes mismatch, current program: -1 checkpoint file: 12 Gromacs binary or parallel settings not identical to previous run. Continuation is exact, but is not guaranteed to be binary identical. Initializing Domain Decomposition on 100 nodes is it a good idea to continue or shall i stick with 60 threads. Like I said, I think it is a bad idea to switch settings haphazardly during the run. As the note indicates, the continuation is exact, but not binary identical. Check the website for what all that means if you're not sure. -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: segmentation fault on gromacs 4.5.5 after mdrun
The output of energy minimization was Potential Energy = -1.42173622068236e+06 Maximum force = 9.00312066109319e+02 on atom 148 Norm of force = 2.06087515037187e+01 Thanks Javier Justin Lemkul wrote On 11/12/13 10:58 AM, cjalmeciga wrote: I run grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr and everything looks fine. I check the nvt.tpr, and temperature is ok. The fact that grompp completes indicates there is nothing syntactically wrong with the input files. Whether or not the content of the .mdp is physically sensible or the input configuration is plausible is an entirely different matter. Please tell us what the exact outcome of the previous energy minimization was (potential energy, maximum force, copied and pasted from screen output or .log file). the real problem is with the mdrun function. could be a problem of the software? You have presented no evidence that would lead anyone to believe the problem is with mdrun. In the vast majority of cases, user input is the problem. -Justin Thanks Javier Justin Lemkul wrote On 11/11/13 11:24 AM, Carlos Javier Almeciga Diaz wrote: Hello evryone, I doing a simulation of a ligand-protein interaction with gromacs 4.5.5. Everything looks fine after I equilibrate the protein-ligand complex. I'm running these commands: grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr mdrun -deffnm nvt Nevertheless, I got this error: Reading file nvt.tpr, VERSION 4.5.5 (double precision) Segmentation fault What should I do? Instantaneous failure typically indicates that the forces are nonsensically high and the constraint algorithm immediately fails. Likely the previous energy minimization did not adequately complete. -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 jalemkul@.umaryland | (410) 706-7441 == -- gmx-users mailing list gmx-users@ 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-request@ . * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- View this message in context: http://gromacs.5086.x6.nabble.com/segmentation-fault-on-gromacs-4-5-5-after-mdrun-tp5012431p5012458.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- == 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 jalemkul@.umaryland | (410) 706-7441 == -- gmx-users mailing list gmx-users@ 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-request@ . * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- View this message in context: http://gromacs.5086.x6.nabble.com/segmentation-fault-on-gromacs-4-5-5-after-mdrun-tp5012431p5012464.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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: segmentation fault on gromacs 4.5.5 after mdrun
On 11/12/13 12:14 PM, cjalmeciga wrote: The output of energy minimization was Potential Energy = -1.42173622068236e+06 Maximum force = 9.00312066109319e+02 on atom 148 Norm of force = 2.06087515037187e+01 OK, reasonable enough. How about a description of what the system is, which force field you chose, how you derived the ligand topology, and the full contents of your .mdp file? -Justin Thanks Javier Justin Lemkul wrote On 11/12/13 10:58 AM, cjalmeciga wrote: I run grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr and everything looks fine. I check the nvt.tpr, and temperature is ok. The fact that grompp completes indicates there is nothing syntactically wrong with the input files. Whether or not the content of the .mdp is physically sensible or the input configuration is plausible is an entirely different matter. Please tell us what the exact outcome of the previous energy minimization was (potential energy, maximum force, copied and pasted from screen output or .log file). the real problem is with the mdrun function. could be a problem of the software? You have presented no evidence that would lead anyone to believe the problem is with mdrun. In the vast majority of cases, user input is the problem. -Justin Thanks Javier Justin Lemkul wrote On 11/11/13 11:24 AM, Carlos Javier Almeciga Diaz wrote: Hello evryone, I doing a simulation of a ligand-protein interaction with gromacs 4.5.5. Everything looks fine after I equilibrate the protein-ligand complex. I'm running these commands: grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr mdrun -deffnm nvt Nevertheless, I got this error: Reading file nvt.tpr, VERSION 4.5.5 (double precision) Segmentation fault What should I do? Instantaneous failure typically indicates that the forces are nonsensically high and the constraint algorithm immediately fails. Likely the previous energy minimization did not adequately complete. -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 jalemkul@.umaryland | (410) 706-7441 == -- gmx-users mailing list gmx-users@ 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-request@ . * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- View this message in context: http://gromacs.5086.x6.nabble.com/segmentation-fault-on-gromacs-4-5-5-after-mdrun-tp5012431p5012458.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- == 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 jalemkul@.umaryland | (410) 706-7441 == -- gmx-users mailing list gmx-users@ 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-request@ . * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- View this message in context: http://gromacs.5086.x6.nabble.com/segmentation-fault-on-gromacs-4-5-5-after-mdrun-tp5012431p5012464.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- == 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] Calculating diffusion coefficient in three dimension
Dear Sir, Thanks for the quick reply. So, I have to declare -type no flag. Isn't it?? and I have recently gone through Justin's membrane protein tutorial, where he has calculated diffusion coefficient for lipids in a membrane by creating an index group for a particular atom. So, here also shall I do the same thing? Moreover, mine is a coarse-grained system. On Tue, Nov 12, 2013 at 9:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 11:25 AM, Venkat Reddy wrote: Then, how to mention the direction for spherical particles Sir? Read g_msd -h again, paying specific attention to the -type flag. -Justin On Tue, Nov 12, 2013 at 7:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 8:55 AM, Venkat Reddy wrote: Thank you sir for the prompt reply. *g_msd -f traj.xtc -s topol.tpr -n msd.ndx -lateral z -o msd.xvg -tu ns* Here I am giving -lateral z (like for membrane simulations). Is it fine for spherical systems also? No. The system is a sphere, so what use is it to calculate motion perpendicular to z when you have lipids moving in all three spatial dimensions? A vesicle is very different from a membrane, in which the lipids move in a plane, thus making -lateral z useful. -Justin On Tue, Nov 12, 2013 at 5:32 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: MSD is 3D by default. Dr. Vitaly V. Chaban On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy venkat...@gmail.com wrote: Dear all, I am simulating a spherical lipid vesicle. I want to calculate the diffusion coefficient for each lipid component in 3D. How to calculate it using g_msd (or any other tool like g_velacc)? Thank you for your concern -- With Best Wishes Venkat Reddy Chirasani -- 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 -- == 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 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] Change in the positon of structural Zinc and calcium ions during MD
Hi Gromacs users, I'm doing protein-Bilayer MD simulations. Enzyme contains structural zinc and calcium ions during Energy minimization, NVT and NPT stage, ions are changing there position even though I applied position restraints for the atoms and ions. Anyone could help me out. Thanks -- View this message in context: http://gromacs.5086.x6.nabble.com/Change-in-the-positon-of-structural-Zinc-and-calcium-ions-during-MD-tp5012467.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Calculating diffusion coefficient in three dimension
On 11/12/13 12:30 PM, Venkat Reddy wrote: Dear Sir, Thanks for the quick reply. So, I have to declare -type no flag. Isn't it?? The options for the -type flag are x, y, or z. You said you wanted the diffusion coefficient in each spatial dimension. That is precisely what this option will do. and I have recently gone through Justin's membrane protein tutorial, where You mean my tutorial :) he has calculated diffusion coefficient for lipids in a membrane by creating an index group for a particular atom. So, here also shall I do the same thing? Moreover, mine is a coarse-grained system. Yes, a representative atom is usually what is passed to g_msd. -Justin On Tue, Nov 12, 2013 at 9:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 11:25 AM, Venkat Reddy wrote: Then, how to mention the direction for spherical particles Sir? Read g_msd -h again, paying specific attention to the -type flag. -Justin On Tue, Nov 12, 2013 at 7:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 8:55 AM, Venkat Reddy wrote: Thank you sir for the prompt reply. *g_msd -f traj.xtc -s topol.tpr -n msd.ndx -lateral z -o msd.xvg -tu ns* Here I am giving -lateral z (like for membrane simulations). Is it fine for spherical systems also? No. The system is a sphere, so what use is it to calculate motion perpendicular to z when you have lipids moving in all three spatial dimensions? A vesicle is very different from a membrane, in which the lipids move in a plane, thus making -lateral z useful. -Justin On Tue, Nov 12, 2013 at 5:32 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: MSD is 3D by default. Dr. Vitaly V. Chaban On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy venkat...@gmail.com wrote: Dear all, I am simulating a spherical lipid vesicle. I want to calculate the diffusion coefficient for each lipid component in 3D. How to calculate it using g_msd (or any other tool like g_velacc)? Thank you for your concern -- With Best Wishes Venkat Reddy Chirasani -- 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 -- == 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
Re: [gmx-users] Change in the positon of structural Zinc and calcium ions during MD
On 11/12/13 12:35 PM, Rama wrote: Hi Gromacs users, I'm doing protein-Bilayer MD simulations. Enzyme contains structural zinc and calcium ions during Energy minimization, NVT and NPT stage, ions are changing there position even though I applied position restraints for the atoms and ions. Anyone could help me out. If the atoms are moving drastically, then the position restraints aren't taking effect, either because they haven't been invoked or they are insufficient. Without your full .mdp file and relevant topology snippets, there's no real way to know. You can check the .log files, too - if there is not an energy component corresponding to position restraints, they haven't been activated. -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] Calculating diffusion coefficient in three dimension
Thanks Justin. So, I have to calculate diffusion coefficient three times (x,y,z) and finally add-up together to get in 3D??? On Tue, Nov 12, 2013 at 11:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 12:30 PM, Venkat Reddy wrote: Dear Sir, Thanks for the quick reply. So, I have to declare -type no flag. Isn't it?? The options for the -type flag are x, y, or z. You said you wanted the diffusion coefficient in each spatial dimension. That is precisely what this option will do. and I have recently gone through Justin's membrane protein tutorial, where You mean my tutorial :) he has calculated diffusion coefficient for lipids in a membrane by creating an index group for a particular atom. So, here also shall I do the same thing? Moreover, mine is a coarse-grained system. Yes, a representative atom is usually what is passed to g_msd. -Justin On Tue, Nov 12, 2013 at 9:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 11:25 AM, Venkat Reddy wrote: Then, how to mention the direction for spherical particles Sir? Read g_msd -h again, paying specific attention to the -type flag. -Justin On Tue, Nov 12, 2013 at 7:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 8:55 AM, Venkat Reddy wrote: Thank you sir for the prompt reply. *g_msd -f traj.xtc -s topol.tpr -n msd.ndx -lateral z -o msd.xvg -tu ns* Here I am giving -lateral z (like for membrane simulations). Is it fine for spherical systems also? No. The system is a sphere, so what use is it to calculate motion perpendicular to z when you have lipids moving in all three spatial dimensions? A vesicle is very different from a membrane, in which the lipids move in a plane, thus making -lateral z useful. -Justin On Tue, Nov 12, 2013 at 5:32 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: MSD is 3D by default. Dr. Vitaly V. Chaban On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy venkat...@gmail.com wrote: Dear all, I am simulating a spherical lipid vesicle. I want to calculate the diffusion coefficient for each lipid component in 3D. How to calculate it using g_msd (or any other tool like g_velacc)? Thank you for your concern -- With Best Wishes Venkat Reddy Chirasani -- 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 -- == 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
Re: [gmx-users] Calculating diffusion coefficient in three dimension
On 11/12/13 1:33 PM, Venkat Reddy wrote: Thanks Justin. So, I have to calculate diffusion coefficient three times (x,y,z) and finally add-up together to get in 3D??? If you just want the overall diffusion constant, that's what g_msd does without any additional options. -Justin On Tue, Nov 12, 2013 at 11:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 12:30 PM, Venkat Reddy wrote: Dear Sir, Thanks for the quick reply. So, I have to declare -type no flag. Isn't it?? The options for the -type flag are x, y, or z. You said you wanted the diffusion coefficient in each spatial dimension. That is precisely what this option will do. and I have recently gone through Justin's membrane protein tutorial, where You mean my tutorial :) he has calculated diffusion coefficient for lipids in a membrane by creating an index group for a particular atom. So, here also shall I do the same thing? Moreover, mine is a coarse-grained system. Yes, a representative atom is usually what is passed to g_msd. -Justin On Tue, Nov 12, 2013 at 9:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 11:25 AM, Venkat Reddy wrote: Then, how to mention the direction for spherical particles Sir? Read g_msd -h again, paying specific attention to the -type flag. -Justin On Tue, Nov 12, 2013 at 7:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 8:55 AM, Venkat Reddy wrote: Thank you sir for the prompt reply. *g_msd -f traj.xtc -s topol.tpr -n msd.ndx -lateral z -o msd.xvg -tu ns* Here I am giving -lateral z (like for membrane simulations). Is it fine for spherical systems also? No. The system is a sphere, so what use is it to calculate motion perpendicular to z when you have lipids moving in all three spatial dimensions? A vesicle is very different from a membrane, in which the lipids move in a plane, thus making -lateral z useful. -Justin On Tue, Nov 12, 2013 at 5:32 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: MSD is 3D by default. Dr. Vitaly V. Chaban On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy venkat...@gmail.com wrote: Dear all, I am simulating a spherical lipid vesicle. I want to calculate the diffusion coefficient for each lipid component in 3D. How to calculate it using g_msd (or any other tool like g_velacc)? Thank you for your concern -- With Best Wishes Venkat Reddy Chirasani -- 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 -- == 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
[gmx-users] Re: Change in the position of structural Zinc and calcium ions during MD
Hi Justin, Below I pasted .mdp file and topology. In .log file I could see energy term for position restraints. .mdp file--- title = NPT Equilibration define = -DPOSRES ; position restraints for protein ; Run parameters integrator = md; leap-frog integrator nsteps = 50; 2 * 50 = 1000 ps (1 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1 ps nstvout = 500 ; save velocities every 1 ps nstenergy = 500 ; save energies every 1 ps nstlog = 500 ; update log file every 1 ps ; Bond parameters continuation= yes ; Restarting after NVT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; More accurate thermostat tc-grps = Protein_CA_ZN DMPC SOL_CL; three coupling groups - more accurate tau_t = 0.50.5 0.5 ; time constant, in ps ref_t = 298298 310 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 5.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5 ; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_DMPC SOL_CL ; Scale COM of reference coordinates refcoord_scaling = com topol.top ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include strong_posre.itp #endif ; Include DMPC topology #include rama4LJ.ff/dmpcLJ.itp ; Include water topology #include rama4LJ.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include rama4LJ.ff/ions.itp ---.log file Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 1.77761e+043.10548e+037.97673e+034.40586e+028.14131e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 2.59758e+042.74092e+04 -2.56846e+03 -4.68637e+05 -1.67418e+05 Position Rest. PotentialKinetic En. Total EnergyTemperature 7.09403e+02 -5.47088e+058.83115e+04 -4.58777e+053.07118e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.00493e+021.00080e+000.0e+00 Thanks -- View this message in context: http://gromacs.5086.x6.nabble.com/Change-in-the-positon-of-structural-Zinc-and-calcium-ions-during-MD-tp5012467p5012474.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Calculating diffusion coefficient in three dimension
Hi Venkat, Can you make it a bit clearer what you actually want? If it is the diffusion of the lipids along the curved surface of the vesicle, rather than simply the overall 3D diffusion, this is not trivial to calculate as I don't believe g_msd will do this for you. This property has been studied before though, so I suggest you search the literature for papers simulating vesicles to see how the lipid diffusion was calculated. Cheers Tom On 11/12/2013 06:35 PM, Justin Lemkul wrote: On 11/12/13 1:33 PM, Venkat Reddy wrote: Thanks Justin. So, I have to calculate diffusion coefficient three times (x,y,z) and finally add-up together to get in 3D??? If you just want the overall diffusion constant, that's what g_msd does without any additional options. -Justin On Tue, Nov 12, 2013 at 11:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 12:30 PM, Venkat Reddy wrote: Dear Sir, Thanks for the quick reply. So, I have to declare -type no flag. Isn't it?? The options for the -type flag are x, y, or z. You said you wanted the diffusion coefficient in each spatial dimension. That is precisely what this option will do. and I have recently gone through Justin's membrane protein tutorial, where You mean my tutorial :) he has calculated diffusion coefficient for lipids in a membrane by creating an index group for a particular atom. So, here also shall I do the same thing? Moreover, mine is a coarse-grained system. Yes, a representative atom is usually what is passed to g_msd. -Justin On Tue, Nov 12, 2013 at 9:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 11:25 AM, Venkat Reddy wrote: Then, how to mention the direction for spherical particles Sir? Read g_msd -h again, paying specific attention to the -type flag. -Justin On Tue, Nov 12, 2013 at 7:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 8:55 AM, Venkat Reddy wrote: Thank you sir for the prompt reply. *g_msd -f traj.xtc -s topol.tpr -n msd.ndx -lateral z -o msd.xvg -tu ns* Here I am giving -lateral z (like for membrane simulations). Is it fine for spherical systems also? No. The system is a sphere, so what use is it to calculate motion perpendicular to z when you have lipids moving in all three spatial dimensions? A vesicle is very different from a membrane, in which the lipids move in a plane, thus making -lateral z useful. -Justin On Tue, Nov 12, 2013 at 5:32 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: MSD is 3D by default. Dr. Vitaly V. Chaban On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy venkat...@gmail.com wrote: Dear all, I am simulating a spherical lipid vesicle. I want to calculate the diffusion coefficient for each lipid component in 3D. How to calculate it using g_msd (or any other tool like g_velacc)? Thank you for your concern -- With Best Wishes Venkat Reddy Chirasani -- 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 -- == 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
Re: mdrun on 8-core AMD + GTX TITAN (was: Re: [gmx-users] Re: Gromacs-4.6 on two Titans GPUs)
Hi Mark and Szilard Thanks for your both suggestions. They are very helpful. Neither run had a PP-PME work distribution suitable for the hardware it was running on (and fixing that for each run requires opposite changes). Adding a GPU and hoping to see scaling requires that there be proportionately more GPU work available to do, *and* enough absolute work to do. mdrun tries to do this, and reports early in the log file, which is one of the reasons Szilard asked to see whole log files - please use a file sharing service to do that. This task involves GPU calculation. We would not see PP-PME work distribution. This is a good hint from the angle of PP-PME work distribution. And I guessed that two GPUs' calculations are fast / or no enough work for GPU calculation, which is aligned with your explanation. Please see logs below again. ONE GPU## http://pastebin.com/B6bRUVSa TWO GPUs## http://pastebin.com/SLAYnejP As you can see, this test was made on the same node regardless of networking. Can the performance be improved say 50% more when 2 GPUs are used on a general task ? If yes, how ? Indeed, as Richard pointed out, I was asking for *full* logs, these summaries can't tell much, the table above the summary entitled R E A L C Y C L E A N D T I M E A C C O U N T I N G as well as other reported information across the log file is what I need to make an assessment of your simulations' performance. Please see below. However, in your case I suspect that the bottleneck is multi-threaded scaling on the AMD CPUs and you should probably decrease the number of threads per MPI rank and share GPUs between 2-4 ranks. After I test all three clusters, I found it may NOT be an issue of AMD cpus. Intel cpus has the SAME scaling issue. However, I am curious as to how you justify the setup of 2-4 ranks sharing GPUs ? Can you please explain it a bit more ? NUMA effects on multi-socket AMD processors are particularly severe; the way GROMACS uses OpenMP is not well suited to them. Using a rank (or two) per socket will greatly reduce those effects, but introduces different algorithmic overhead from the need to do DD and explicitly communicate between ranks. (You can see the latter in your .log file snippets below.) Also, that means the parcel of PP work available from a rank to give to the GPU is smaller, which is the opposite of what you'd like for GPU performance and/or scaling. We are working on a general solution for this and lots of related issues in the post-5.0 space, but there is a very hard limitation imposed by the need to amortize the cost of CPU-GPU transfer by having lots of PP work available to do. Is this reason why the scaling of two GPUs won't happen because of smaller PP workload ? From the implication, I am wondering if we can increase PP workload through parameters in a mdp file. The question is what parameters are mostly related to PP workload ? Would you please give more specific suggestions ? NOTE: The GPU has 20% more load than the CPU. This imbalance causes performance loss, consider using a shorter cut-off and a finer PME grid. This note needs to be addressed before maximum throughput is achieved and the question of scaling is worth considering. Ideally, Wait GPU local should be nearly zero, achieved as suggested above. Note that launch+force+mesh+wait is the sum of gpu total! But much of the information needed is higher up the log file, and the whole question is constrained by things like rvdw. From the note, it clearly suggested a shorter cut-off and a finer PME grid. I am not sure how to set up a finer PME grid but I am able to set up shorter cut-offs . However, it is risky to do so based on others' reports. Indeed, I see differences among tests for 1 GPU. Here cutoffs refer to rlist, rvdw and rcoulomb. I found that the smaller values of cutoffs, the faster computations. The question is how small they can go because it is interesting to know if these different cutoffs generate equally good simulations. As to two GPUs, when I set up larger cut-offs, these two GPUs in the same node had been very busy. However, the outcome in such a configuration is worse in terms of ns/day and time. So what dose a finer PME grid mean, with respect to GPU workload ? You mention the sum of GPU total is launch + force + mesh + wait.I thought PME mesh is carried out by CPU instead of GPU. Do I miss something here ? I thought GPU is responsible for the calculation of short-ranged non-bonded force whereas CPU is responsible for that of bonded and PME long-ranged force. Can you clarify it here ? Also, would rvdw play an important role in improving the performance of GPU calculation ? Unfortunately you didn't copy the GPU timing stuff here! Roughly, all the performance gain you are seeing here is eliminating most of the single-GPU wait gpu term by throwing
Re: [gmx-users] Re: Change in the position of structural Zinc and calcium ions during MD
On 11/12/13 1:47 PM, Rama wrote: Hi Justin, Below I pasted .mdp file and topology. In .log file I could see energy term for position restraints. .mdp file--- title = NPT Equilibration define = -DPOSRES ; position restraints for protein ; Run parameters integrator = md; leap-frog integrator nsteps = 50; 2 * 50 = 1000 ps (1 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1 ps nstvout = 500 ; save velocities every 1 ps nstenergy = 500 ; save energies every 1 ps nstlog = 500 ; update log file every 1 ps ; Bond parameters continuation= yes ; Restarting after NVT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; More accurate thermostat tc-grps = Protein_CA_ZN DMPC SOL_CL; three coupling groups - more accurate tau_t = 0.50.5 0.5 ; time constant, in ps ref_t = 298298 310 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 5.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5 ; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_DMPC SOL_CL ; Scale COM of reference coordinates refcoord_scaling = com topol.top ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include strong_posre.itp #endif ; Include DMPC topology #include rama4LJ.ff/dmpcLJ.itp ; Include water topology #include rama4LJ.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include rama4LJ.ff/ions.itp Do you have appropriate [position_restraints] assigned in this topology? None of the above, as shown, pertains to the ions, and the only relevant #ifdef block that would be triggered by -DPOSRES is for the protein. -Justin ---.log file Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 1.77761e+043.10548e+037.97673e+034.40586e+028.14131e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 2.59758e+042.74092e+04 -2.56846e+03 -4.68637e+05 -1.67418e+05 Position Rest. PotentialKinetic En. Total EnergyTemperature 7.09403e+02 -5.47088e+058.83115e+04 -4.58777e+053.07118e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.00493e+021.00080e+000.0e+00 Thanks -- View this message in context: http://gromacs.5086.x6.nabble.com/Change-in-the-positon-of-structural-Zinc-and-calcium-ions-during-MD-tp5012467p5012474.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- == 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
[gmx-users] help about ibi
Hi: When I am running the ibi procedure, I get the following error message: A coordinate in file conf.gro does not contain a '.' Additionally, I check the coordinate file of confout.gro in step_001. It showed that 'nan' symbol appeared in confout.gro. What is wrong with this? How can I fix it? I am very appreciating for anyone's help. Best Wishes! Zhicheng Guo-- 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] Calculating diffusion coefficient in three dimension
Dear Justin and Piggot, Thanks for the suggestions. Actually, I have constructed a CG lipid vesicle by placing lipids in random conformation in a simulation box. My lipid system is heterogeneous, i.e., it has different types of lipids (POPC,CHOLESTEROL,PPC...etc). Some of them occupy the outer layer of vesicle (POPC), and some stay in the intermediate region (CHOL). So, I want to calculate the diffusion rates of these lipids. Since POPC forms the surface (polar heads interacting with water and their tails points to the core), I suppose we have to calculate 2D diffusion for POPC. For the lipids in the core, they can diffuse in 3-dimension. So, it requires a 3D diffusion coefficient for these core lipids. How to calculate 2D and 3D diffusion coeff.? Hope I am clear. On Wed, Nov 13, 2013 at 12:58 AM, Thomas Piggot t.pig...@soton.ac.ukwrote: Hi Venkat, Can you make it a bit clearer what you actually want? If it is the diffusion of the lipids along the curved surface of the vesicle, rather than simply the overall 3D diffusion, this is not trivial to calculate as I don't believe g_msd will do this for you. This property has been studied before though, so I suggest you search the literature for papers simulating vesicles to see how the lipid diffusion was calculated. Cheers Tom On 11/12/2013 06:35 PM, Justin Lemkul wrote: On 11/12/13 1:33 PM, Venkat Reddy wrote: Thanks Justin. So, I have to calculate diffusion coefficient three times (x,y,z) and finally add-up together to get in 3D??? If you just want the overall diffusion constant, that's what g_msd does without any additional options. -Justin On Tue, Nov 12, 2013 at 11:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 12:30 PM, Venkat Reddy wrote: Dear Sir, Thanks for the quick reply. So, I have to declare -type no flag. Isn't it?? The options for the -type flag are x, y, or z. You said you wanted the diffusion coefficient in each spatial dimension. That is precisely what this option will do. and I have recently gone through Justin's membrane protein tutorial, where You mean my tutorial :) he has calculated diffusion coefficient for lipids in a membrane by creating an index group for a particular atom. So, here also shall I do the same thing? Moreover, mine is a coarse-grained system. Yes, a representative atom is usually what is passed to g_msd. -Justin On Tue, Nov 12, 2013 at 9:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 11:25 AM, Venkat Reddy wrote: Then, how to mention the direction for spherical particles Sir? Read g_msd -h again, paying specific attention to the -type flag. -Justin On Tue, Nov 12, 2013 at 7:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 8:55 AM, Venkat Reddy wrote: Thank you sir for the prompt reply. *g_msd -f traj.xtc -s topol.tpr -n msd.ndx -lateral z -o msd.xvg -tu ns* Here I am giving -lateral z (like for membrane simulations). Is it fine for spherical systems also? No. The system is a sphere, so what use is it to calculate motion perpendicular to z when you have lipids moving in all three spatial dimensions? A vesicle is very different from a membrane, in which the lipids move in a plane, thus making -lateral z useful. -Justin On Tue, Nov 12, 2013 at 5:32 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: MSD is 3D by default. Dr. Vitaly V. Chaban On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy venkat...@gmail.com wrote: Dear all, I am simulating a spherical lipid vesicle. I want to calculate the diffusion coefficient for each lipid component in 3D. How to calculate it using g_msd (or any other tool like g_velacc)? Thank you for your concern -- With Best Wishes Venkat Reddy Chirasani -- 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 -- == 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] Re: Bilayer COM removal issue: Large VCM
Hi All, Any suggestions? Thanks, On Mon, Nov 11, 2013 at 12:38 AM, rajat desikan rajatdesi...@gmail.comwrote: Hi All, I am experiencing a few problems in membrane simulations wrt COM removal. I downloaded a 400 ns pre-equilibrated Slipid-DMPC membrane with all the accompanying files. I then carried out the following steps: 1) energy minimization 2) NVT Eq - 100 ps 3) NPT Eq - 250 ps (Berendsen temp, Pres coupling) Then I used g_select to select the upper and lower DMPC leaflets. The then carried out a 250 ps NPT eq again. The only change was: comm-grps= SOL DMPC == comm-grps= SOL upper lower On every step in log file, I get the following message: *Step Time Lambda 124000 248.00.0 Large VCM(group lower): -0.00051, -0.00515, -0.00652, Temp-cm: 8.11828e+29 Energies (kJ/mol)U-BProper Dih. Improper Dih. LJ-14 Coulomb-147.23818e+044.19778e+046.46641e+024.54801e+03 -1.45245e+05 LJ (SR)LJ (LR) Disper. corr. Coulomb (SR) Coul. recip.2.79689e+04 -3.78407e+03 -2.10679e+03 -5.84134e+05 -8.87497e+04 PotentialKinetic En. Total EnergyTemperature Pres. DC (bar)-6.76497e+051.76468e+05 -5.00029e+05 3.10424e+02 -1.05704e+02 Pressure (bar) Constr. rmsd -1.85927e+02 6.42934e-06* *Large VCM(group lower): -0.00187, -0.00369, 0.00032, Temp-cm: 2.02076e+29 Large VCM(group lower): -0.00725, -0.00278, -0.00549, Temp-cm: 1.05988e+30Large VCM(group lower): 0.00020, 0.00308, -0.00176, Temp-cm: 1.48126e+29Large VCM(group lower): -0.00541, 0.00546, -0.00166, Temp-cm: 7.24656e+29 Large VCM(group lower): -0.00220, 0.00362, -0.00741, Temp-cm: 8.53812e+29Large VCM(group lower): 0.00140, -0.00160, 0.00029, Temp-cm: 5.39679e+28Large VCM(group lower): -0.00056, -0.00293, -0.00364, Temp-cm: 2.59422e+29 Large VCM(group lower): -0.00172, -0.00260, 0.00494, Temp-cm: 3.99945e+29Large VCM(group lower): 0.00252, 0.00594, 0.00068, Temp-cm: 4.93342e+29* *DD step 124999 vol min/aver 0.702 load imb.: force 1.3% pme mesh/force 0.636* I do not know what to make of it. There are no issues when I remove COM for the entire system. I have seen this issue come up a few times in the archives too, but I didn't find a satisfactory solution since the bilayer was very well equilibrated. I would appreciate any suggestions. Thank you. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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
