RE: [gmx-users] Unable to download Gromacs source tar file
Hi, Thanks for your reply. But the problem still persists. Even now I am not able to download. -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham Sent: Fri 6/7/2013 8:14 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Unable to download Gromacs source tar file They're fine now. Perhaps the FTP server was offline briefly. Mark On Fri, Jun 7, 2013 at 7:41 AM, Bhamy Maithry Shenoy bhamymait...@aero.iisc.ernet.in wrote: Hi, I would like to use Gromacs for MD simulation of biomolecules. But I am not able to download any of the source files from the link http://www.gromacs.org/Downloads Can anyone please help. Thanks and regards, Maithry -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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] Unable to download Gromacs source tar file
They're still fine. There must be a problem at your end, I'm afraid. Mark On Sat, Jun 8, 2013 at 10:46 AM, Bhamy Maithry Shenoy bhamymait...@aero.iisc.ernet.in wrote: Hi, Thanks for your reply. But the problem still persists. Even now I am not able to download. -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham Sent: Fri 6/7/2013 8:14 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Unable to download Gromacs source tar file They're fine now. Perhaps the FTP server was offline briefly. Mark On Fri, Jun 7, 2013 at 7:41 AM, Bhamy Maithry Shenoy bhamymait...@aero.iisc.ernet.in wrote: Hi, I would like to use Gromacs for MD simulation of biomolecules. But I am not able to download any of the source files from the link http://www.gromacs.org/Downloads Can anyone please help. Thanks and regards, Maithry -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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: Steepest LINCS WARNING
Seems something http://www.gromacs.org/Documentation/Terminology/Blowing_Up, probably because there is something nonsensical about your starting configuration. Try to simplify things, visualize the configuration, don't ignore warnings. Mark On Sat, Jun 8, 2013 at 7:10 AM, maggin maggin.c...@gmail.com wrote: when I first run enery minimization in vacuum, then add water model, (I use GROMOS96 53a6 force field, and spce water model) EM in water model: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps= 2000 Step=0, Dmax= 5.0e-03 nm, Epot= -3.51690e+05 Fmax= 2.16580e+04, atom= 21005 Step=1, Dmax= 5.0e-03 nm, Epot= -3.60975e+05 Fmax= 1.24353e+04, atom= 3050 Step=2, Dmax= 6.0e-03 nm, Epot= -3.73328e+05 Fmax= 8.74189e+03, atom= 3050 Step=3, Dmax= 7.2e-03 nm, Epot= -3.85332e+05 Fmax= 5.54552e+03, atom= 3050 Step=4, Dmax= 8.6e-03 nm, Epot= -3.98300e+05 Fmax= 3.03988e+03, atom= 20120 Step=5, Dmax= 1.0e-02 nm, Epot= -4.13757e+05 Fmax= 1.75853e+03, atom= 29072 Step=6, Dmax= 1.2e-02 nm, Epot= -4.29896e+05 Fmax= 1.55053e+03, atom= 29072 Step=7, Dmax= 1.5e-02 nm, Epot= -4.42239e+05 Fmax= 1.28428e+03, atom= 29072 Step=8, Dmax= 1.8e-02 nm, Epot= -4.53744e+05 Fmax= 1.40998e+03, atom= 920 Step=9, Dmax= 2.1e-02 nm, Epot= -4.61547e+05 Fmax= 4.89215e+03, atom= 520 Step= 10, Dmax= 2.6e-02 nm, Epot= -4.63542e+05 Fmax= 5.75251e+03, atom= 516 Step= 11, Dmax= 3.1e-02 nm, Epot= -4.64658e+05 Fmax= 5.56526e+03, atom= 520 Step 12, time 0.024 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.004301, max 0.126066 (between atoms 512 and 516) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 512516 39.00.1472 0.1565 0.1390 514518 38.50.1467 0.1558 0.1390 516520 38.80.1472 0.1557 0.1390 518520 38.70.1471 0.1550 0.1390 511514 39.70.1466 0.1561 0.1390 511512 40.10.1470 0.1561 0.1390 Step= 13, Dmax= 1.9e-02 nm, Epot= -4.67377e+05 Fmax= 3.11093e+03, atom= 5116 Step= 15, Dmax= 1.1e-02 nm, Epot= -4.68747e+05 Fmax= 2.97283e+03, atom= 520 Step= 16, Dmax= 1.3e-02 nm, Epot= -4.70028e+05 Fmax= 3.63802e+03, atom= 516 Step= 17, Dmax= 1.6e-02 nm, Epot= -4.71166e+05 Fmax= 4.03533e+03, atom= 520 Step= 18, Dmax= 1.9e-02 nm, Epot= -4.71943e+05 Fmax= 4.96009e+03, atom= 516 Step= 19, Dmax= 2.3e-02 nm, Epot= -4.72558e+05 Fmax= 5.15705e+03, atom= 520 Step= 21, Dmax= 1.4e-02 nm, Epot= -4.75111e+05 Fmax= 1.55977e+03, atom= 511 Step= 22, Dmax= 1.7e-02 nm, Epot= -4.75363e+05 Fmax= 5.38247e+03, atom= 582 Step= 23, Dmax= 2.0e-02 nm, Epot= -4.77689e+05 Fmax= 3.75868e+03, atom= 159 Step= 25, Dmax= 1.2e-02 nm, Epot= -4.79001e+05 Fmax= 2.54107e+03, atom= 159 Step= 26, Dmax= 1.4e-02 nm, Epot= -4.79210e+05 Fmax= 4.39836e+03, atom= 159 Step= 27, Dmax= 1.7e-02 nm, Epot= -4.80268e+05 Fmax= 3.94950e+03, atom= 159 Step= 29, Dmax= 1.0e-02 nm, Epot= -4.81704e+05 Fmax= 1.36796e+03, atom= 159 Step= 30, Dmax= 1.2e-02 nm, Epot= -4.82183e+05 Fmax= 4.55734e+03, atom= 159 Step= 31, Dmax= 1.5e-02 nm, Epot= -4.83601e+05 Fmax= 2.65995e+03, atom= 159 Step= 33, Dmax= 8.9e-03 nm, Epot= -4.84347e+05 Fmax= 2.05512e+03, atom= 159 Step= 34, Dmax= 1.1e-02 nm, Epot= -4.84811e+05 Fmax= 3.30097e+03, atom= 159 Step= 35, Dmax= 1.3e-02 nm, Epot= -4.85461e+05 Fmax= 3.18540e+03, atom= 159 Step= 36, Dmax= 1.5e-02 nm, Epot= -4.85605e+05 Fmax= 4.31161e+03, atom= 159 Step= 37, Dmax= 1.9e-02 nm, Epot= -4.85983e+05 Fmax= 4.53453e+03, atom= 159 Step= 39, Dmax= 1.1e-02 nm, Epot= -4.87596e+05 Fmax= 1.03948e+03, atom= 366 Step= 40, Dmax= 1.3e-02 nm, Epot= -4.87792e+05 Fmax= 4.95272e+03, atom= 159 Step= 41, Dmax= 1.6e-02 nm, Epot= -4.89343e+05 Fmax= 2.61653e+03, atom= 159 Step= 43, Dmax= 9.6e-03 nm, Epot= -4.89881e+05 Fmax= 2.44528e+03, atom= 159 Step= 44, Dmax= 1.2e-02 nm, Epot= -4.90124e+05 Fmax= 3.33456e+03, atom= 159 Step= 45, Dmax= 1.4e-02 nm, Epot= -4.90496e+05 Fmax= 3.58399e+03, atom= 159 Step= 47, Dmax= 8.3e-03 nm, Epot= -4.91468e+05 Fmax= 6.25094e+02, atom= 366 writing lowest energy coordinates. Back Off! I just backed up em_constrain.gro to ./#em_constrain.gro.2# Steepest Descents converged to Fmax 1000 in 48 steps Potential Energy = -4.9146806e+05 Maximum force = 6.2509442e+02 on atom 366 Norm of force = 6.6710007e+01 LINCS WARNING relative constraint deviation after LINCS: rms 0.004301, max 0.126066 (between atoms 512 and 516) ATOM512 HD2 ARG A 156 -13.495 -6.447 -3.087 1.00 0.00 H ATOM516 NH1 ARG A 156 -14.923 -9.012 -5.069 1.00 0.00 N Befor EM in vacuum, there are 4 LINCS WARNING; now there are only one, But I have no idea what can I do, to kill this LINCS WARNING? Thank you very much! maggin -- View this message in
Fwd: [gmx-users] Eigenvector and eigenvalues
Hi Tsjerk, [I am reposting it since my previous attachment was unable to proceed I guess] Thank you for the reply. I am sorry but I don't have the snapshots with me as my system was formatted and I lost that information. However, I performed PCA again on Calpha atoms and this time my matrix is 5976X5976 wherein 1992 are my total number of calpha atoms. So, yes indeed I did something foolish in the previous case to have got that result. However, I will try to look at it and find my mistake so as to not repeat it again. I would be really grateful if you could help me with my another naive query. I wanted to see the movie of first few eigenvectors as individual and also separately. I know I can extract that with the help of g_anaeig but as I did PCA on only calpha atoms, all I get in the projection of first eigenvector is the calpha dots. Is there any way, I can visualise the projection of whole protein on that particular eigenvector? Secondly, if I want to see the projection along first 10 eigenvectors and last 10 eigenvectors (slow modes and fast modes), how could I proceed because when I choose -first 1 -last 10, it gives me individual pdb files corresponding to the eigenvectors. Third, as can be judged by my absolute naivety, I did a 2d projection on PC 1 and PC 2. I can visualise that plot in grace as a 2d plot. An example file is appended herein. I know each dot might correspond to a particular conformation in the trajectory but I really have no idea as to how to interpret the results and draw conclusions from these 2d plots and also 3d pdb projections. Could you please guide me in the right direction to understand these 2d plots and infer the significant results? Kind regards, Ankita On Thu, Jun 6, 2013 at 2:49 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Ankita, Please provide the commands you've run and the screen output from g_covar. Cheers, Tsjerk On Thu, Jun 6, 2013 at 3:44 PM, Ankita naithani ankitanaith...@gmail.com wrote: Hi, I wanted to know about the eigenvectors and eigenvalues. I recently performed the principal component analysis (only the backbone into consideration) on a trajectory of 2000 residues. I obtained 15641 eigenvectors and 17928 eigenvalues. There is a difference in the number, which I am not quite sure off (perhaps that has to do with eigenvalue for each eigenvector, and the eigenvector has 3 co-ordinates x,y,z. I know I may be wrong completely but since there are 15641 eigenvectors, then shouldn't there by only 15641 eigenvalues for those eigenvectors) My second problem lies that I am trying to extract information or say RMSF values for the first 10 eigenvectors (10 slowest modes) and the last 10 eigenvectors (fastest modes) and there I face segmentation fault. I can get information on the first 10 but when I try last 10 with the command as follows: g_anaeig -v eigenvec.trr -eig eigenval.xvg -rmsf eig_rmsf.xvg -first 15631 [where -first should have the starting eigenvector ] (I choose, 15631 since I want the plot for last 10 but I get segmentation fault, which is also to do with the fact that the eigenval.xvg has 17928 values. This number doesn't match and so, maybe the plot is from 15631-17928). This has further confused me about the slowest and fastest modes (and somehow I do need information on the first 10 slowest modes and 10 fastest modes). In a broad way, the slowest modes would be the ones with high eigenvalues say, first 10 eigenvectors in eigenval.xvg would give the slowest 10 modes and the last 10 in eigenval.xvg should give the fastest 10 modes. Here, again I feel quite confused because eigenval.xvg has 17928 entries and in the legend, it says that x axis is the eigenvector index and y axis is eigenvalue index so it leaves me quite perplexed about the problem. I am sorry for this extremely long and confusing post, but any help in this regard would be really beneficial. Kind regards, Ankita -- Ankita Naithani -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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 -- Ankita Naithani -- Ankita Naithani -- Ankita Naithani -- gmx-users mailing list
Re: [gmx-users] Unable to download Gromacs source tar file
I too cannot download (tried with 3.3 4.5.5 4.6 and 4.5.7). Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Sat, Jun 8, 2013 at 4:05 PM, Mark Abraham mark.j.abra...@gmail.comwrote: They're still fine. There must be a problem at your end, I'm afraid. Mark On Sat, Jun 8, 2013 at 10:46 AM, Bhamy Maithry Shenoy bhamymait...@aero.iisc.ernet.in wrote: Hi, Thanks for your reply. But the problem still persists. Even now I am not able to download. -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham Sent: Fri 6/7/2013 8:14 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Unable to download Gromacs source tar file They're fine now. Perhaps the FTP server was offline briefly. Mark On Fri, Jun 7, 2013 at 7:41 AM, Bhamy Maithry Shenoy bhamymait...@aero.iisc.ernet.in wrote: Hi, I would like to use Gromacs for MD simulation of biomolecules. But I am not able to download any of the source files from the link http://www.gromacs.org/Downloads Can anyone please help. Thanks and regards, Maithry -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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 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] Unable to download Gromacs source tar file
I just downloaded the 4.5.7 tarball to a machine in Australia. Mark On Sat, Jun 8, 2013 at 1:23 PM, Chandan Choudhury iitd...@gmail.com wrote: I too cannot download (tried with 3.3 4.5.5 4.6 and 4.5.7). Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Sat, Jun 8, 2013 at 4:05 PM, Mark Abraham mark.j.abra...@gmail.com wrote: They're still fine. There must be a problem at your end, I'm afraid. Mark On Sat, Jun 8, 2013 at 10:46 AM, Bhamy Maithry Shenoy bhamymait...@aero.iisc.ernet.in wrote: Hi, Thanks for your reply. But the problem still persists. Even now I am not able to download. -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham Sent: Fri 6/7/2013 8:14 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Unable to download Gromacs source tar file They're fine now. Perhaps the FTP server was offline briefly. Mark On Fri, Jun 7, 2013 at 7:41 AM, Bhamy Maithry Shenoy bhamymait...@aero.iisc.ernet.in wrote: Hi, I would like to use Gromacs for MD simulation of biomolecules. But I am not able to download any of the source files from the link http://www.gromacs.org/Downloads Can anyone please help. Thanks and regards, Maithry -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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 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] Unable to download Gromacs source tar file
As a work-around, you can try to get archives from https://github.com/gromacs/gromacs/tags (but these will not quite match the official tarballs - but in ways that don't matter for simulating). Mark On Sat, Jun 8, 2013 at 1:54 PM, Mark Abraham mark.j.abra...@gmail.comwrote: I just downloaded the 4.5.7 tarball to a machine in Australia. Mark On Sat, Jun 8, 2013 at 1:23 PM, Chandan Choudhury iitd...@gmail.comwrote: I too cannot download (tried with 3.3 4.5.5 4.6 and 4.5.7). Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Sat, Jun 8, 2013 at 4:05 PM, Mark Abraham mark.j.abra...@gmail.com wrote: They're still fine. There must be a problem at your end, I'm afraid. Mark On Sat, Jun 8, 2013 at 10:46 AM, Bhamy Maithry Shenoy bhamymait...@aero.iisc.ernet.in wrote: Hi, Thanks for your reply. But the problem still persists. Even now I am not able to download. -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham Sent: Fri 6/7/2013 8:14 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Unable to download Gromacs source tar file They're fine now. Perhaps the FTP server was offline briefly. Mark On Fri, Jun 7, 2013 at 7:41 AM, Bhamy Maithry Shenoy bhamymait...@aero.iisc.ernet.in wrote: Hi, I would like to use Gromacs for MD simulation of biomolecules. But I am not able to download any of the source files from the link http://www.gromacs.org/Downloads Can anyone please help. Thanks and regards, Maithry -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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 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] Unable to download Gromacs source tar file
On 08.06.2013 10:46, Bhamy Maithry Shenoy wrote: Hi, Thanks for your reply. But the problem still persists. Even now I am not able to download. Can you download from this link? ftp://ftp.gromacs.org/pub/gromacs/ -- 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] Unable to download Gromacs source tar file
Thanks a lot. I could download from this link. Is is the latest version? -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham Sent: Sat 6/8/2013 5:27 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Unable to download Gromacs source tar file As a work-around, you can try to get archives from https://github.com/gromacs/gromacs/tags (but these will not quite match the official tarballs - but in ways that don't matter for simulating). Mark On Sat, Jun 8, 2013 at 1:54 PM, Mark Abraham mark.j.abra...@gmail.comwrote: I just downloaded the 4.5.7 tarball to a machine in Australia. Mark On Sat, Jun 8, 2013 at 1:23 PM, Chandan Choudhury iitd...@gmail.comwrote: I too cannot download (tried with 3.3 4.5.5 4.6 and 4.5.7). Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Sat, Jun 8, 2013 at 4:05 PM, Mark Abraham mark.j.abra...@gmail.com wrote: They're still fine. There must be a problem at your end, I'm afraid. Mark On Sat, Jun 8, 2013 at 10:46 AM, Bhamy Maithry Shenoy bhamymait...@aero.iisc.ernet.in wrote: Hi, Thanks for your reply. But the problem still persists. Even now I am not able to download. -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham Sent: Fri 6/7/2013 8:14 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Unable to download Gromacs source tar file They're fine now. Perhaps the FTP server was offline briefly. Mark On Fri, Jun 7, 2013 at 7:41 AM, Bhamy Maithry Shenoy bhamymait...@aero.iisc.ernet.in wrote: Hi, I would like to use Gromacs for MD simulation of biomolecules. But I am not able to download any of the source files from the link http://www.gromacs.org/Downloads Can anyone please help. Thanks and regards, Maithry -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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 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 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. --
RE: [gmx-users] Unable to download Gromacs source tar file
I could not download from the mentioned link. -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Mirco Wahab Sent: Sat 6/8/2013 5:42 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Unable to download Gromacs source tar file On 08.06.2013 10:46, Bhamy Maithry Shenoy wrote: Hi, Thanks for your reply. But the problem still persists. Even now I am not able to download. Can you download from this link? ftp://ftp.gromacs.org/pub/gromacs/ -- 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 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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] why mass and charge is zero?
Hello: I generate a ligand toplogy by ACPYPE with amber GAFF. However, I found that in the ligandGMX.itp file, in the atomtypes section, the mass and charge are all zero, like: [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb NT NT 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 however, in the atoms sections, I found: [ atoms ] ; nr type resi res atom cgnr charge mass ; qtot bond_type 26 NT 1 UKA N10 26-0.719301 14.01000 ; qtot -7.758 I am a little bit confused for this. Does anybody have any idea for it? thank you very much best Albert -- 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] why mass and charge is zero?
On 2013-06-08 17:28, Albert wrote: Hello: I generate a ligand toplogy by ACPYPE with amber GAFF. However, I found that in the ligandGMX.itp file, in the atomtypes section, the mass and charge are all zero, like: [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb NT NT 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 however, in the atoms sections, I found: [ atoms ] ; nr type resi res atom cgnr charge mass ; qtot bond_type 26 NT 1 UKA N10 26-0.719301 14.01000 ; qtot -7.758 I am a little bit confused for this. Does anybody have any idea for it? the ones in the atoms section are the ones that are used UNLESS they are not given, in which case the defaults are used. thank you very much best Albert -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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: Unable to download Gromacs source tar file
Date: Sat, 8 Jun 2013 13:57:51 +0200 From: Mark Abraham mark.j.abra...@gmail.com Subject: Re: [gmx-users] Unable to download Gromacs source tar file To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: camnumasy_p5tqoarcvgat1qd0wb2dwfh9ouhvfk-83vauh8...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 As a work-around, you can try to get archives from https://github.com/gromacs/gromacs/tags (but these will not quite match the official tarballs - but in ways that don't matter for simulating). Or use google to find the tarball: https://www.google.com/search?q=intitle:%22index+of%22+gromacs-4.6.1.tar.gz Christoph Mark On Sat, Jun 8, 2013 at 1:54 PM, Mark Abraham mark.j.abra...@gmail.comwrote: I just downloaded the 4.5.7 tarball to a machine in Australia. Mark On Sat, Jun 8, 2013 at 1:23 PM, Chandan Choudhury iitd...@gmail.comwrote: I too cannot download (tried with 3.3 4.5.5 4.6 and 4.5.7). Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Sat, Jun 8, 2013 at 4:05 PM, Mark Abraham mark.j.abra...@gmail.com wrote: They're still fine. There must be a problem at your end, I'm afraid. Mark On Sat, Jun 8, 2013 at 10:46 AM, Bhamy Maithry Shenoy bhamymait...@aero.iisc.ernet.in wrote: Hi, Thanks for your reply. But the problem still persists. Even now I am not able to download. -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham Sent: Fri 6/7/2013 8:14 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Unable to download Gromacs source tar file They're fine now. Perhaps the FTP server was offline briefly. Mark On Fri, Jun 7, 2013 at 7:41 AM, Bhamy Maithry Shenoy bhamymait...@aero.iisc.ernet.in wrote: Hi, I would like to use Gromacs for MD simulation of biomolecules. But I am not able to download any of the source files from the link http://www.gromacs.org/Downloads Can anyone please help. Thanks and regards, Maithry -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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 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 -- 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
Re: [gmx-users] Unable to download Gromacs source tar file
On 08.06.2013 14:39, Bhamy Maithry Shenoy wrote: Can you download from this link? ftp://ftp.gromacs.org/pub/gromacs/ I could not download from the mentioned link. Then, your provider/router and/or your network configuration is blocking FTP port traffic (Port 21), but not HTTP port traffic (Port 80). M. -- 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] why mass and charge is zero?
On 06/08/2013 06:56 PM, David van der Spoel wrote: the ones in the atoms section are the ones that are used UNLESS they are not given, in which case the defaults are used. IC. thank you very much. Albert -- 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] GPU ECC question
Hello: Recently I found a strange question about Gromacs-4.6.2 on GPU workstaion. In my GTX690 machine, when I run md production I found that the ECC is on. However, in my another GTX590 machine, I found the ECC was off: 4 GPUs detected: #0: NVIDIA GeForce GTX 590, compute cap.: 2.0, ECC: no, stat: compatible #1: NVIDIA GeForce GTX 590, compute cap.: 2.0, ECC: no, stat: compatible #2: NVIDIA GeForce GTX 590, compute cap.: 2.0, ECC: no, stat: compatible #3: NVIDIA GeForce GTX 590, compute cap.: 2.0, ECC: no, stat: compatible moreover, there is only two GTX590 in the machine, I don't know why Gromacs claimed 4 GPU detected. However, in my another Linux machine which also have two GTX590, Gromacs-4.6.2 only find 2 GPU, and ECC is still off. I am just wondering: (1) why in GTX690 the ECC can be on while it is off in my GTX590? I compiled Gromacs with the same options and the same version of intel compiler (2) why in machines both of physically installed two GTX590 cards, one of them was detected with 4 GPU while the other was claimed contains two GPU? thank you very much best Albert -- 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] Eigenvector and eigenvalues
Hi Ankita, It is important to use the correct names for things. The projection is the (scalar) inner product of the configuration (coordinates) with the eigenvector. This is also named the score of the configuration on the selected eigenvector. With g_anaeig -proj you get the projection. Each configuration of a trajectory has a projection, and you can plot them over time, or plot the projection on one eigenvector against another (-2d). You can also make a 3D plot of three selected eigenvectors (-3d), which is written out as a PDB file. The projection is not a structure, and you can't have a movie of structures. What you can do is extract the structures corresponding to the extreme projections (-extr). Those are always written per eigenvector. Since the eigenvectors are uncorrelated, the extremes are not defined for combinations of them. It is also possible to filter a trajectory on a set of eigenvectors. That will give a trajectory of (unphysical) structures, in which the projections on the non-selected eigenvectors are set to zero. This filtering is a matrix operation, using the matrix of selected eigenvectors and the corresponding atoms of the trajectory. Because the matrix of eigenvectors is derived from C-alpha atoms only in your case, it is not possible to get anything else out of it. Hope it helps, Tsjerk On Sat, Jun 8, 2013 at 1:06 PM, Ankita naithani ankitanaith...@gmail.comwrote: Hi Tsjerk, [I am reposting it since my previous attachment was unable to proceed I guess] Thank you for the reply. I am sorry but I don't have the snapshots with me as my system was formatted and I lost that information. However, I performed PCA again on Calpha atoms and this time my matrix is 5976X5976 wherein 1992 are my total number of calpha atoms. So, yes indeed I did something foolish in the previous case to have got that result. However, I will try to look at it and find my mistake so as to not repeat it again. I would be really grateful if you could help me with my another naive query. I wanted to see the movie of first few eigenvectors as individual and also separately. I know I can extract that with the help of g_anaeig but as I did PCA on only calpha atoms, all I get in the projection of first eigenvector is the calpha dots. Is there any way, I can visualise the projection of whole protein on that particular eigenvector? Secondly, if I want to see the projection along first 10 eigenvectors and last 10 eigenvectors (slow modes and fast modes), how could I proceed because when I choose -first 1 -last 10, it gives me individual pdb files corresponding to the eigenvectors. Third, as can be judged by my absolute naivety, I did a 2d projection on PC 1 and PC 2. I can visualise that plot in grace as a 2d plot. An example file is appended herein. I know each dot might correspond to a particular conformation in the trajectory but I really have no idea as to how to interpret the results and draw conclusions from these 2d plots and also 3d pdb projections. Could you please guide me in the right direction to understand these 2d plots and infer the significant results? Kind regards, Ankita On Thu, Jun 6, 2013 at 2:49 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Ankita, Please provide the commands you've run and the screen output from g_covar. Cheers, Tsjerk On Thu, Jun 6, 2013 at 3:44 PM, Ankita naithani ankitanaith...@gmail.com wrote: Hi, I wanted to know about the eigenvectors and eigenvalues. I recently performed the principal component analysis (only the backbone into consideration) on a trajectory of 2000 residues. I obtained 15641 eigenvectors and 17928 eigenvalues. There is a difference in the number, which I am not quite sure off (perhaps that has to do with eigenvalue for each eigenvector, and the eigenvector has 3 co-ordinates x,y,z. I know I may be wrong completely but since there are 15641 eigenvectors, then shouldn't there by only 15641 eigenvalues for those eigenvectors) My second problem lies that I am trying to extract information or say RMSF values for the first 10 eigenvectors (10 slowest modes) and the last 10 eigenvectors (fastest modes) and there I face segmentation fault. I can get information on the first 10 but when I try last 10 with the command as follows: g_anaeig -v eigenvec.trr -eig eigenval.xvg -rmsf eig_rmsf.xvg -first 15631 [where -first should have the starting eigenvector ] (I choose, 15631 since I want the plot for last 10 but I get segmentation fault, which is also to do with the fact that the eigenval.xvg has 17928 values. This number doesn't match and so, maybe the plot is from 15631-17928). This has further confused me about the slowest and fastest modes (and somehow I do need information on the first 10 slowest modes and 10 fastest modes). In a broad way, the slowest modes would be the ones with high
