Re: [gmx-users] Coordination number
Sir Thank you for the reply. The higher graph is also broader and I thought should then give a higher coordination number. Does gromacs use the box density? does it not use 4*pi*r2*g(r) for calculating rdf (thats what I read in a paper where the authors have used gromacs for simulation and analyses)?where is the density coming then? Thank you On Wed, Aug 21, 2013 at 4:20 AM, Dallas Warren dallas.war...@monash.eduwrote: Peak can be higher, but if it is narrower the total area can still be less. Remember it is an area under the curve. Additionally, that overall system / box density that you are using may be different too, so that will make a difference. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Venkat Reddy Sent: Monday, 19 August 2013 8:11 PM To: Discussion list for GROMACS users Subject: [gmx-users] Coordination number Dear Gromacs Users, I have a query about the g_rdf utility. I have two different systems of water with Ionic Liquid 1 and Ionic Liquid 2. When I plot the rdf using g_rdf -f x_gro.pdb -s x.pdb -n rdf.ndx -o rdf1.xvg/rdf2.xvg -cn rdf1_cn.xvg/rdf2_cn.xvg -rdf res_com where rdf1/rdf2 is for water distribution around Ionic liquid 1/2, the rdf1.xvg clearly shows a higher first peak g(r) than the rdf2.xvg. Both also have minima at the same distance. However, the coordination number at first minima from rdf1_cn.xvg is lesser than the same from rd2_cn.xvg. How is this possible? If the peak is larger, the integration of it should give a higher value right? Please help. -- 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 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] g_hydorder error
Dear all, I am using following command in gromacs version 4.5.5: g_hydorder -f *.xtc -s *.tpr -n *.ndx -o file1.xpm file2.xpm But getting following error: Internal error in pbc_dx, set_pbc has not been called In my mdp file, I have set pbc to xyz I have searched the archive and found that similar issue was raised earlier in the past and was filed as a bug. I have seen bugzilla and found the status to be closed. Please help me resolve the problem. Any help is appreciated -- 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] g_hydorder error
On 8/26/13 8:27 AM, Nidhi Katyal wrote: Dear all, I am using following command in gromacs version 4.5.5: g_hydorder -f *.xtc -s *.tpr -n *.ndx -o file1.xpm file2.xpm But getting following error: Internal error in pbc_dx, set_pbc has not been called In my mdp file, I have set pbc to xyz I have searched the archive and found that similar issue was raised earlier in the past and was filed as a bug. I have seen bugzilla and found the status to be closed. Please help me resolve the problem. Any help is appreciated Upgrade to 4.6.3 and try again. -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] Gromacs 4.6.3 Installation Issues,
probably u do not have CUDA. If you are not really interested in performing simulations using GPU, you can set -DGMX_GPU=off during cmake On Sat, Aug 24, 2013 at 12:15 PM, No One not1morepara...@yahoo.com wrote: hi, i'm having difficulties installing gromacs by creating static links to the libraries for fftw3. i am currently running: cygwin1.7.24-1 cmake2.8.11.2-1 fftw33.3.3-1 this is the input that i'm attempting to utilize and flags errors (and some combination there of): cmake FFTW3F_INCLUDE_DIR=C:\FFTW\fftw-3.3.3\api FFTWF_LIBRARIES=C:\FFTW\fftw-3.3.3\.libs this is my error output: /cygdrive/c/gromacs/gromacs-4.6.3/build-cmake $ cmake FFTW3F_INCLUDE_DIR=C:\FFTW\fftw-3.3.3\api FFTWF_LIBRARIES=C:\FFTW\fftw-3.3.3\.libs .. -- Could NOT find CUDA (missing: CUDA_CUDART_LIBRARY) (found suitable version 5.5, minimum required is 3.2) -- Enabling native GPU acceleration CMake Error at cmake/FindFFTW.cmake:122 (message): The FFTW library /usr/local/lib/libfftw3f.a cannot be used with shared libraries. Provide a different FFTW library by setting FFTWF_LIBRARY. If you don't have a different one, recompile FFTW with --enable-shared or --with-pic. Or disable shared libraries for Gromacs by setting BUILD_SHARED_LIBS to no. Note: Disabling shared libraries requires up to 10x as much disk space. Call Stack (most recent call first): CMakeLists.txt:948 (find_package) any assistance would be appreciated. thanks. -- 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
[gmx-users] error with g_dist
Hello all, I am trying to find the distance between 2 centres of mass using g_dist. I use the command: g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n index.ndx but i get the error: Fatal error: Molecule in topology has atom numbers below and above natoms (1707). You are probably trying to use a trajectory which does not match the first 1707 atoms of the run input file. You can make a matching run input file with tpbconv. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I tried using tpbconv like suggested. But that did not help. I really need help on this as my submission deadline is getting closer and this is the last simulation I need.. Thank you so much in advance Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/error-with-g-dist-tp5010736.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] error with g_dist
On 8/26/13 4:05 PM, chinnu657 wrote: Hello all, I am trying to find the distance between 2 centres of mass using g_dist. I use the command: g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n index.ndx but i get the error: Fatal error: Molecule in topology has atom numbers below and above natoms (1707). You are probably trying to use a trajectory which does not match the first 1707 atoms of the run input file. You can make a matching run input file with tpbconv. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I tried using tpbconv like suggested. But that did not help. I really need help on this as my submission deadline is getting closer and this is the last simulation I need.. The most likely explanation is that you did not save groups correctly using xtc-grps in the .mdp file. In the absence of a description of what you're trying to measure, the contents of the index groups, and the gmxcheck output on the .xtc file, there's little anyone can do to help. -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: error with g_dist
I'm basically trying to see how the distance between the ligand and protein changes with time using their centres of mass and the only way I've come across is by using g_dist. I'm pasting the contents from the terminal after the doing a gmxcheck on the md_0_1.xtc file which is my .xtc file from the production simulation. Checking file md_0_1.xtc Reading frame 0 time0.000 # Atoms 33037 Precision 0.001 (nm) Last frame 1000 time 2000.000 Item#frames Timestep (ps) Step 10012 Time 10012 Lambda 0 Coords10012 Velocities 0 Forces 0 Box 10012 can I attach the index.ndx file again? Was this what you were looking for? index.ndx http://gromacs.5086.x6.nabble.com/file/n5010738/index.ndx thank you, chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/error-with-g-dist-tp5010736p5010738.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: error with g_dist
On 8/26/13 4:39 PM, chinnu657 wrote: I'm basically trying to see how the distance between the ligand and protein changes with time using their centres of mass and the only way I've come across is by using g_dist. I'm pasting the contents from the terminal after the doing a gmxcheck on the md_0_1.xtc file which is my .xtc file from the production simulation. Checking file md_0_1.xtc Reading frame 0 time0.000 # Atoms 33037 Precision 0.001 (nm) Last frame 1000 time 2000.000 Item#frames Timestep (ps) Step 10012 Time 10012 Lambda 0 Coords10012 Velocities 0 Forces 0 Box 10012 can I attach the index.ndx file again? Was this what you were looking for? index.ndx http://gromacs.5086.x6.nabble.com/file/n5010738/index.ndx Better would be for you to actually tell us what groups you chose (actual screen output from the selection would be best), rather than leave us to scroll through and guess. If md_0_1.xtc has the whole system (33037 atoms), in principle that error should not have occurred. -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: error with g_dist
Oh, sorry sorry. I see what your asking. I asked for 2 groups. One being the protein and one being the ligand (JZ4) screenshot.png http://gromacs.5086.x6.nabble.com/file/n5010740/screenshot.png sorry, you may have to zoom in. I'm not sure how to snip on linux still. Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/error-with-g-dist-tp5010736p5010740.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: error with g_dist
On 8/26/13 4:58 PM, chinnu657 wrote: Oh, sorry sorry. I see what your asking. I asked for 2 groups. One being the protein and one being the ligand (JZ4) screenshot.png http://gromacs.5086.x6.nabble.com/file/n5010740/screenshot.png sorry, you may have to zoom in. I'm not sure how to snip on linux still. Copying and pasting text works well. I understand what the list of groups is, but what groups *exactly* did you choose? -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: error with g_dist
1 and 13 Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/error-with-g-dist-tp5010736p5010742.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: error with g_dist
On 8/26/13 5:05 PM, chinnu657 wrote: 1 and 13 I don't see how this error would be possible unless you accidentally chose group 22. Choosing 1 and 13 should be perfectly viable. -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: error with g_dist
No, I chose 1 and 13. I just tried again, but the error is still the same.. Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/error-with-g-dist-tp5010736p5010744.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: error with g_dist
On 8/26/13 5:35 PM, chinnu657 wrote: No, I chose 1 and 13. I just tried again, but the error is still the same.. Send me your .tpr file, a coordinate file (.pdb or .gro) of the system, and your index file off-list and I will look into it. -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: error with g_dist
I've copy, pasted the text after selection: eading file md_0_1.tpr, VERSION 4.5.5 (single precision) Group 0 ( System) has 33037 elements Group 1 (Protein) has 1693 elements Group 2 ( Protein-H) has 1301 elements Group 3 (C-alpha) has 163 elements Group 4 ( Backbone) has 489 elements Group 5 ( MainChain) has 653 elements Group 6 ( MainChain+Cb) has 805 elements Group 7 (MainChain+H) has 815 elements Group 8 ( SideChain) has 878 elements Group 9 (SideChain-H) has 648 elements Group10 (Prot-Masses) has 1693 elements Group11 (non-Protein) has 31344 elements Group12 ( Other) has15 elements Group13 (JZ4) has15 elements Group14 ( CL) has 6 elements Group15 ( Water) has 31323 elements Group16 (SOL) has 31323 elements Group17 ( non-Water) has 1714 elements Group18 (Ion) has 6 elements Group19 (JZ4) has15 elements Group20 ( CL) has 6 elements Group21 ( Water_and_ions) has 31329 elements Group22 (Protein_JZ4) has 1708 elements Select a group: 1 13 Selected 1: 'Protein' Select a group: Selected 13: 'JZ4' Reading frame 0 time0.000 -- View this message in context: http://gromacs.5086.x6.nabble.com/error-with-g-dist-tp5010736p5010745.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: error with g_dist
md_0_1.tpr http://gromacs.5086.x6.nabble.com/file/n5010747/md_0_1.tpr - production simulation .tpr file 3HTB_clean.pdb http://gromacs.5086.x6.nabble.com/file/n5010747/3HTB_clean.pdb - .pdb file after removing hz4 coordinates JZ4.pdb http://gromacs.5086.x6.nabble.com/file/n5010747/JZ4.pdb - jz4 coordinates md_0_1.gro http://gromacs.5086.x6.nabble.com/file/n5010747/md_0_1.gro -production simulation .gro file index.ndx http://gromacs.5086.x6.nabble.com/file/n5010747/index.ndx - index file Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/error-with-g-dist-tp5010736p5010747.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: error with g_dist
On 8/26/13 5:47 PM, chinnu657 wrote: md_0_1.tpr http://gromacs.5086.x6.nabble.com/file/n5010747/md_0_1.tpr - production simulation .tpr file 3HTB_clean.pdb http://gromacs.5086.x6.nabble.com/file/n5010747/3HTB_clean.pdb - .pdb file after removing hz4 coordinates JZ4.pdb http://gromacs.5086.x6.nabble.com/file/n5010747/JZ4.pdb - jz4 coordinates md_0_1.gro http://gromacs.5086.x6.nabble.com/file/n5010747/md_0_1.gro -production simulation .gro file index.ndx http://gromacs.5086.x6.nabble.com/file/n5010747/index.ndx - index file The command: echo 1 13 | g_dist -s md_0_1.tpr -f md_0_1.gro -n index.ndx works perfectly fine for me with 4.5.5. Try it and see what your outcome is. -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: error with g_dist
Mine still gives me the same error. I don't quite understand why since it's giving u the right output. Im using the same version as you too. If you do not mind, could you give me the .xvg file? So that I can use it as a result. Simultaneously, I'll see what I can do to solve the problem with your help? Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/error-with-g-dist-tp5010736p5010749.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: error with g_dist
On 8/26/13 6:03 PM, chinnu657 wrote: Mine still gives me the same error. I don't quite understand why since it's giving u the right output. Im using the same version as you too. My guess would be that your installation is buggy, usually the fault of a bad/outdated compiler. Without significantly more detail about how your software was compiled and installed, it's simply conjecture, but a probable cause. You could also try installing version 4.6.3, but I doubt the problem lies in Gromacs and rather the compilers, libraries, etc. available on your system. If you do not mind, could you give me the .xvg file? So that I can use it as a result. Simultaneously, I'll see what I can do to solve the problem with your help? I would be far more concerned with the fact that your Gromacs installation produces spurious error messages - who knows what else might be wrong? Me providing you with a single number, which is not necessarily representative of any ensemble, does you no good. I'm also not comfortable with providing someone with a data file so they can use it for a submission (as you called it earlier), which seems to imply some sort of assignment, given that it appears you are working through one of my tutorials. -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: error with g_dist
ok that's ok then. this was the school system. so I can't really reinstall it. I'll try and use a cluster. Hopefully, it works. thanks a lot Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/error-with-g-dist-tp5010736p5010751.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: error with g_dist
I won't be submitting these though. just letting you know. I just need to explain how all of these can be achieved. Just clarifying. But thank you for all the help you've provided. It's been very valuable help. Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/error-with-g-dist-tp5010736p5010752.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] Coordination number
I don't know how g_rdf script uses any density to calculate the cumulative number RDF, I have always calculated the RDF then done the integration myself to determine the coordination number. You need to look at the data you have in front of you, work out the density yourself, integrate yourself etc to understand and see what is actually happening. That would be much faster than asking here on the emailing list. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Venkat Reddy Sent: Monday, 26 August 2013 10:02 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Coordination number Sir Thank you for the reply. The higher graph is also broader and I thought should then give a higher coordination number. Does gromacs use the box density? does it not use 4*pi*r2*g(r) for calculating rdf (thats what I read in a paper where the authors have used gromacs for simulation and analyses)?where is the density coming then? Thank you On Wed, Aug 21, 2013 at 4:20 AM, Dallas Warren dallas.war...@monash.eduwrote: Peak can be higher, but if it is narrower the total area can still be less. Remember it is an area under the curve. Additionally, that overall system / box density that you are using may be different too, so that will make a difference. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Venkat Reddy Sent: Monday, 19 August 2013 8:11 PM To: Discussion list for GROMACS users Subject: [gmx-users] Coordination number Dear Gromacs Users, I have a query about the g_rdf utility. I have two different systems of water with Ionic Liquid 1 and Ionic Liquid 2. When I plot the rdf using g_rdf -f x_gro.pdb -s x.pdb -n rdf.ndx -o rdf1.xvg/rdf2.xvg -cn rdf1_cn.xvg/rdf2_cn.xvg -rdf res_com where rdf1/rdf2 is for water distribution around Ionic liquid 1/2, the rdf1.xvg clearly shows a higher first peak g(r) than the rdf2.xvg. Both also have minima at the same distance. However, the coordination number at first minima from rdf1_cn.xvg is lesser than the same from rd2_cn.xvg. How is this possible? If the peak is larger, the integration of it should give a higher value right? Please help. -- 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 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 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
