[gmx-users] g_rmsdist error hi (-1000.000000) <= lo (0.000000)
Hi all, I'm trying to use this tool with the following command (selecting the backbone atoms: 366 atoms in total) g_rmsdist -s 1.pdb -f traj_fit.trr -rms But the programs stop with the following error: Program g_rmsdist, VERSION 4.5.4 Source code file: matio.c, line: 953 Fatal error: hi (-1000.00) <= lo (0.00) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Could you please help me? Thanks Andrea -- ¯¯¯¯ Andrea Carotti Dipartimento di Chimica e Tecnologia del Farmaco Università di Perugia Via del Liceo, 1 06123 Perugia, Italy phone: +39 075 585 5169 fax: +39 075 585 5161 www http://gryphus.chimfarm.unipg.it personal www http://iris.chimfarm.unipg.it/users/andcar -- 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_sas with pbc
Hi all, I've already simulated 27 organic molecules in a cubic solvent box. Now I would like to calculate the SAS of this system. I've a tpr and a trr with only the molecules inside (without water). I'm using gromacs 4.0.5. I've added the box dimension infos to the trr using the command: trjconv -f ../../original_multi3000.pdb -o new.trr -s reference.pdb -box 7.3973 7.3973 7.3973 In the reference.pdb I've also the CRYST informations. I've modified the gmx_sas.c to bypass the check that turn off automatically the PBC if solvent molecules are not present. Unfortunately I've seen that the results with and without taking into account the PBC are identical. So my questions are: 1) Is it possible to use the g_sas tool to calculate the SAS of this kind of system? 2) There are some tricks or trasformations or missing informations in my input(s) that I could fill before running the analysis? 3)Should I use another type of box? Trasform the trajectory with some pbc keywords (I've also tried -ur compact without luck)... Thanks in advance and sorry for the long message Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Variance in ED
Dear Dr. Wassenaar, many thanks for your kind reply. Andrea -- Andrea Carotti Dipartimento di Chimica e Tecnologia del Farmaco Università di Perugia Via del Liceo, 1 06123 Perugia, Italy phone: +39 075 585 5169 fax: +39 075 585 5161 www http://rpg.unipg.it personal www http://iris.chimfarm.unipg.it/users/andcar ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Variance in ED
Hi all, perhaps a silly question but i didn't find the correct way to calculate the variance explained by each eigenvec in ED analysis. Could someone point me out to a correct tool/option to use. I'm using gmx v3.3. Many thanks Andrea -- ¯¯¯¯¯¯¯¯ Andrea Carotti Dipartimento di Chimica e Tecnologia del Farmaco Università di Perugia Via del Liceo, 1 06123 Perugia, Italy phone: +39 075 585 5169 fax: +39 075 585 5161 www http://rpg.unipg.it personal www http://iris.chimfarm.unipg.it/users/andcar ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] xpm to ascii
Hi all, I would like to have a txt file from an xpm matrix generated by g_rms or g_cluster. Someone has already done this? I've seen in the previous posts some hints about hacking the code or scripts usefull for g_covar...but I'm not so confortable and expert to do such things without a step by step guru guide... Thanks Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rms
> So does the -Rmat option not produce a human-readable text file? Hi, unfortunately I can't see this option in g_rms. I'm using the v 3.3.1 and also on the reference page online there is not -Rmat. Am i missing something? Thanks Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rms
Hi again, > If you read g_rms -h like I suggested last time, you'll see that -f2 and > -s serve the same purpose with the former using a trajectory and the > latter a single structure. That document doesn't say what happens when > you use both... but the operation you're trying to do doesn't need both! the -h option is my standard first step when i use all the gmx-tools and I've read and done it like every time. I've tried to use -f2 option without using the -s and it comes out with the error "topol.tpr not found" so it's not "so optional", but it's needed also when using the -f2 option.. I've alsto tried to use the -s with my traj without using the -f2 option but it creates a matrix 2200x2200. However the problem still remain unsolved or misunderstanded. If i use the my only working command line g_rms -f 2200.pdb -f2 33.pdb -s ref.pdb -n -o -m -bin I obtain a rmsd.xvg with 2 columns. So, which is the meaning of that value? a mean of all the rmsd calculated for that frame in respect to the other 33 refs? Thanks Andrea -- Andrea Carotti Dipartimento di Chimica e Tecnologia del Farmaco Via del Liceo, 1 06123 Perugia, Italy phone: +39 075 585 5169 fax: +39 075 585 5161 www http://rpg.unipg.it personal www http://iris.chimfarm.unipg.it/users/andcar ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rms
Hi, > You should be getting such a 2200x33 matrix. My guess is that the > command line or files that you're using are not what you think they > are :-) my command line is g_rms -f 2200.pdb -f2 33.pdb -s ref.pdb -n -o -m -bin Note that the pdbs (traj and ref) have the same number of atoms (same structure). During the calculation i can see that it is creating the 2200x33 matrix, but on the rmsd.xvg i find only two columns. From the xpm and dat files i can't extract the matrix (i don't know) to a text file. I hope this could clarify better my question Thanks Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_rms
Hi and thanks for answering to my previous question. Now I'm calculating the rmsd between two trajectories (-f2 option). One is made by 2200 frames and the other has 33 frames..Now I've some doubt about the output (rmsd.xvg), cause this file has only two columns with 2200 rows ...i was imaging that it should have 2200 rows and 33 columns, am I wrong? The second question is something that is already been asked before..it could be usefull to obtain the matrix 2200 x 33 in a human readable file. Is it possible without hacking the code? Perhaps using external scripts? Thanks a lot again Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_cluster questions
Hi all, I'm using this tool to cluter 2200 structures in this way: fitting on the backbone, rmsd calculated on key residues (10) of the Binding site. Now I created the correct group in the index file and using the g_cluster giving the trajectory as input i can only choose one group for fitting and rmsd calculation..So I've tried also to fit the trajectory before to use it in g_cluster with the option -fit (to jump the fitting step and choose directly the group for the rmsd calculation; i've tried also -fit no) but it seems that the program ignore it (on screen, during the group selection it asks for the "fitting and Rmsd group" and on -fit line i can see yes)...SO my next strategy is been to calculate the xpm matrix with g_rms, fitting on the backbone and calculating the rmsd values on the Bindingsite group. Then I've used the xpm as input in the g_cluster, but it asks me however for a group for the LSfitting..could someone explain me this behaviour? Is my procedure correct for my purpose? Is normal that g_cluster does not accept the -fit option? Thanks Andrea -- ¯¯¯¯¯¯¯¯ Andrea Carotti Dipartimento di Chimica e Tecnologia del Farmaco Via del Liceo, 1 06123 Perugia, Italy phone: +39 075 585 5169 fax: +39 075 585 5161 www http://rpg.unipg.it personal www http://iris.chimfarm.unipg.it/users/andcar ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] psf 2 top
Hi all, I've performed my MD simulations using the charmm FF and NAMD (so pdb,psf and dcd files). Now i would like to use the great GMX analysis tools. I've successfully converted the dcd file in trr (using catDCD). Now the next step I'd like to do is the psf to top conversion. I've seen on the vmd site that a top2psf script is present but it not do the reverse conv that i need. I would prefer to not pass through pdbs.I would like to do this to not loose corrispondences of atoms and to not miss parameters for not typical residues that I'm using (like phosphrilated serines). Is there someone that could help me on this topic? Thanks in advance Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_hbond -contact option
Hi all, I have found this interesting option in g_hbond, and I would like to know something more about it. How does it work? Which is the difference with other tools like g_dist? Thanks to all Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: g_hbond error "Your computational box has shrunk too much"
The problem is that i don't have an energy file cause this time I'm using gromacs only for analyze my trajs...so I don't know how to make the plot you suggested. Now perhaps I've found a workaroud using trjconv with the option -box 1 1 1 set, but I' don't know if this could be correct. (I've checked the ouput traj in VMD and seems fine, and with it g_hbond is working) Best Andrea -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: g_hbond error "Your computational box has shrunk too much"
> Is it correct? Did you plot the box volume as a function of time? > You can use g_hbond for different stretches of the trajectory and > combine the results manually. > -- Thanks for the fast reply. I'm only trying to monitor the hbond formation with the " basic" command g_hbond -f m93_newtraj.trr -s topol.tpr -n and giving to the groups selection two different parts of my protein (i've made an index file)..and then the programs suddenly stop. the default output (-num) should be the total number of hbond per frame. Please help me again Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_hbond error "Your computational box has shrunk too much"
Hi all, I'm beginning to analyze my trajectories, everything works fine with (g_rmsf, g_saltbr ...) but when i try to use g_hbond I receive this error: -- Program g_hbond, VERSION 3.3.1 Source code file: gmx_hbond.c, line: 631 Fatal error: Your computational box has shrunk too much. g_hbond can not handle this situation, sorry. --- Is this a bug or a problme with my system? Is there the possibility to avoid this problem in some way? THANKS Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Reordering problem AMBER to GROMACS
Hi all gmxers, I'm trying to analyze an amber dynamic (v.8) with the gromacs tools (last version). Sorry in advance for the long message. To do so, I'm trying to generate also a tpr file (needed by some tools). My procedure is being to convert all the MD in multiple pdb format. So I have extracted the first frame to generate a .top file. So I've converted the pdb res atom names that didn't match the OPLS-All atom FF (6th option): sed -e "/ATOM/s/HIE/HIS/g" -e "/ATOM/s/NME/NAC/g" -e "/ATOM/s/HB3 GLU/HB1 GLU/g" -e "/ATOM/s/HG3 GLU/HG1 GLU/g" -e "/ATOM/s/HB3 LEU/HB1 LEU/g" -e "/ATOM/s/HB3 ASP/HB1 ASP/g" -e "/ATOM/s/HG3/HG1/g" -e "/ATOM/s/HG13 ILE/HG11 ILE/g" -e "/ATOM/s/HD3 LYS/HD1 LYS/g" -e "/ATOM/s/HE3 LYS/HE1 LYS/g" -e "/ATOM/s/HD3 ARG/HD1 ARG/g" -e "/ATOM/s/HD3 PRO/HD1 PRO/g" -e "/ATOM/s/HA3 GLY/HA1 GLY/g" pdb_orig.pdb > pdb_ok.pdb This made pdb2gmx work without problems generating .top and .gro files...so with these files i will generate a tpr file. Now the problem is that the atom order is different between the gro file and the multiple pdb file (the original trajectory). Is there a way to make the trajectory (original) in the correct order (that comes from the gromacs new files)? If yes, please tell me a solution in a step-by-step way. Many thanks to all Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Paralellization limit?
Hi Carsten, thanks for your quick reply. Could you plese confrim me that gromacs 3.3.1 works and compile fine with mpich 2.x? Cause this is the first time that I hear that from a user and I'll go ahead on this way instead of usin LAM. Thanks again Andrea - Original Message - From: "Carsten Kutzner" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" Sent: Wednesday, April 19, 2006 2:15 PM Subject: Re: [gmx-users] Paralellization limit? Hi Andrea, Andrea Carotti wrote: Hi all, I'm trying to simulate a system with two identical proteins (42aa each one), solvent spc (18430 mols) and 6 ions NA+...for a total of ~56100 atoms. Now the "problem" is that if I run the MD on 4 nodes everything works fine, but when I try to use 6 or 8 cpus the process stops on the master and continue only on the last two slaves (4 cpus, the systems are dual xeon). The problem is that I can't find any error message on the log files. I've tried using the d.dppc benchmark files, and all goes fine with 2-4-6 and 8 cpus. So my question is: is there a limit of parallelization in gromacs depending on the simulated system? I'm using gromacs 3.3.1, mpich 1.2.5.2 and fftw 2.1.5. I have encountered similar problems when using mpich 1.2.x on Ethernet. Upgrading to mpich-2.x or using LAM solved the problems. There is only a parallelisation limit in the sense that using more CPUs does not always result in faster execution. 56 k atoms should run happily on 8 CPUs. Good luck, Carsten ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Paralellization limit?
Hi all, I'm trying to simulate a system with two identical proteins (42aa each one), solvent spc (18430 mols) and 6 ions NA+...for a total of ~56100 atoms. Now the "problem" is that if I run the MD on 4 nodes everything works fine, but when I try to use 6 or 8 cpus the process stops on the master and continue only on the last two slaves (4 cpus, the systems are dual xeon). The problem is that I can't find any error message on the log files. I've tried using the d.dppc benchmark files, and all goes fine with 2-4-6 and 8 cpus. So my question is: is there a limit of parallelization in gromacs depending on the simulated system? I'm using gromacs 3.3.1, mpich 1.2.5.2 and fftw 2.1.5. Thanks in advance Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] replica exchange doubt
Hi all, I've another question, in the manual (page 39) a REMD calculator is mentioned. Where is it? I've tried to search it on the website without success. Thanks again Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] replica exchange doubt
Thanks to all for the quick clarifications. Andrea - Original Message - From: "Xavier Periole" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" Sent: Tuesday, April 11, 2006 1:55 PM Subject: Re: [gmx-users] replica exchange doubt Andrea Carotti wrote: Hi all gmx-ers, I have a doubt concerning the REMD setup. Let's say I want to use 12 cpus to make a REMD at 2 different temp 300 and 400K of the same system. Should I prepare every tpr file with the -np option set to 6? and then run the mdrun with -np 12 -multi -s 300.tpr 400.tpr -replica X -reseed? I don't think that running each replica on more than one cpu is implemented !! The last doubt: is it possible/supported to make a REMD with an Umbrella sampling (a force between 2 centers of mass)associated? Thanks a lot -- -- Xavier Periole - Ph.D. Dept. of Biophysical Chemistry / MD Group Univ. of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands Tel: +31-503634329 Fax: +31-503634398 email: [EMAIL PROTECTED] web-page: http://md.chem.rug.nl/~periole -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] replica exchange doubt
Hi all gmx-ers, I have a doubt concerning the REMD setup. Let's say I want to use 12 cpus to make a REMD at 2 different temp 300 and 400K of the same system. Should I prepare every tpr file with the -np option set to 6? and then run the mdrun with -np 12 -multi -s 300.tpr 400.tpr -replica X -reseed? The last doubt: is it possible/supported to make a REMD with an Umbrella sampling (a force between 2 centers of mass)associated? Thanks a lot Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to install MPI version of Gromacs on a Linux Cluster
Hi, Here http://www.gromacs.org/documentation/howtos/mpich_howto.html you'll find an interesting solution for you.. Bye Andrea - Original Message - From: "Shankar Prasad Kanaujia" <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]> Cc: Sent: Monday, March 27, 2006 8:03 AM Subject: [gmx-users] How to install MPI version of Gromacs on a Linux Cluster Dear Gromacs Users, I am a new user of gromcas. But I have problem in installing mpi version of gromacs on a cluster which has the following configurations: 1. It has 8 nodes. 2. Each node has PIV 3.4 GHz and having 2 GB RAM. 3. Redhat Enterprise Linux 4.0 4. MPICH-1.2.5 version I do not know how to install MPI version of Gromacs. What files I need to edit. I request you all to kindly tell me the steps to install MPI version of gromacs on the cluster. (Note: I am able to install gromacs on a single processor machine.) I would be highly grateful for the same. Thanking you. Yours Sincerely, -- Shankar Prasad Kanaujia Ph.D Student Bioinformatics Center, Department of SERC IISc, Bangalore - 12 Mobile: 9845631581 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] AFM pulling
Hi all, I am a bit confused about some points on the manual (section 6.1, manual 3.2). I f i define two groups: one that will be pulled and the other as reference group; then the force constant and the rate, must i define also the afm_dir and the afm_unit? In my mind, if i define two groups (centers) in the space, they will define a vector where the spring will be placed and then I'll set also the strenght of pulling and its movement (rate). Could someone give me some hints or comments about? Many thanks Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs 3.3 manual
Thank you for the fast answer. Please let me (us) know, when it will be fixed. Thanks Andrea - Original Message - From: "David van der Spoel" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" Sent: Friday, March 17, 2006 11:23 AM Subject: Re: [gmx-users] Gromacs 3.3 manual Andrea Carotti wrote: Hi all, I'm trying to create the manual from the cvs repository suing the command: cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co manual and then using the README file on that dir created. But I'm encountering a lot of errors and problem ending with a creation of an unreadable pdf. I'm using a linux box with Fedora core 2. Could someone share with me a working pdf or ps manual? or eventually guide me through a successfull creation of it? sorry itäs broken right now. will fix it ASAP. Many thanks in advance Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Gromacs 3.3 manual
Hi all, I'm trying to create the manual from the cvs repository suing the command: cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co manual and then using the README file on that dir created. But I'm encountering a lot of errors and problem ending with a creation of an unreadable pdf. I'm using a linux box with Fedora core 2. Could someone share with me a working pdf or ps manual? or eventually guide me through a successfull creation of it? Many thanks in advance Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
