[gmx-users] converting Desmond trajectories to Gromacs
Dear Sir/Madam I am running simulations on a membrane protein using Desmond and I want to calculate area per lipid for the entire trajectory. I can convert the trajectories to those of Gromacs using VMD. What else do I need in order to calculate area per lipid using Gromacs? Thanking you Regards -- Nidhi Jatana Senior Research Fellow Bioinformatics Center Sri Venkateswara College (University of Delhi) Dhaula Kuan New Delhi-110021. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] converting Desmond trajectories to Gromacs
Dear Sir/Madam I am running simulations on a membrane protein using Desmond and I want to calculate area per lipid for the entire trajectory. I can convert the trajectories to those of Gromacs using VMD. What else do I need in order to calculate area per lipid using Gromacs? Thanking you Regards -- Nidhi Jatana Senior Research Fellow Bioinformatics Center Sri Venkateswara College (University of Delhi) Dhaula Kuan New Delhi-110021. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] problem regarding installation of gromacs-4.5.5
Dear Sir/Madam I am not getting any errors while compiling. Its all running fine. Thanking you Regards -- Nidhi Jatana Senior Research Fellow Bioinformatics Center Sri Venkateswara College (University of Delhi) Dhaula Kuan New Delhi-110021. -- 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] problem regarding installation of gromacs-4.5.5
Dear Sir/Madam Thanks for all the help. I have removed the older version of gromacs and the new one also and hve reinstalled gromacs again. But I am still encountering the same problem. I am unable to figure out. First I removed the installed gromacs and all the links. The set of commands that I have given to install gromacs are as folllows: * ./configure --enable-mpi --program-suffix=_mpi make make mdrun -j 8 make install make install-mdrun make links export PATH=$PATH:/usr/local/gromacs/bin/GMXRC echo $PATH* Please note that initially I had problems while compiling gromacs so I reinstalled fftw (version 3.3.2) by giving in the following commands: *cd fftw-3.3.2 ./configure --enable-float --enable-sse --enable-shared make make install* Please help. I am unable to figure out what's wrong with the installation. Thanking you Regards -- Nidhi Jatana Senior Research Fellow Bioinformatics Center Sri Venkateswara College (University of Delhi) Dhaula Kuan New Delhi-110021. -- 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] problem regarding installation of gromacs-4.5.5
Dear Sir/Madam I checked up in the system, there was one version of gromacs in /opt/bio/. I removed that and I reinstalled gromacs using the following commands: tar -xvf gromacs-4.5.5.tar.gz cd gromacs-4.5.5 ./configure --program-suffix="_mpi" make make mdrun -j 8 make install make install-mdrun make links But now, its not running any commands. I made links and I made entry into the .bashrc file by putting up the following command: export GMXRC=/usr/local/gromacs/bin/GMXRC Now, I am unable to run any coomand of gromacs. What could be the possible solution. Thanking you Regards -- Nidhi Jatana Senior Research Fellow Bioinformatics Center Sri Venkateswara College (University of Delhi) Dhaula Kuan New Delhi-110021. -- 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] problem regarding installation of gromacs-4.5.5
Dear Sir/Madam This is Nidhi Jatana. I downloaded the lastest version of gromacs i.e. 4.5.5 from the link (ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.5.tar.gz) and have installed it but whenever I am trying to run any of the programs, its showing me the version to be 4.0.5. For example, I was trying to run the lysozyme tutorial and while running genion i gave in the command: genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn 8 and getting this as the output (not posted the entire output) ":-) G R O M A C S (-: Glycine aRginine prOline Methionine Alanine Cystine Serine :-) VERSION 4.0.5 (-:" I have installed it thrice, but the problem persists. Infact, I am getting an error (Fatal error: No such moleculetype NA) while running minimization. And when I saw the user-mailing lists, it shows me that there is some problem with the version. What should I do? Should I install the previous version? Thanking you Regards -- Nidhi Jatana Senior Research Fellow Bioinformatics Center Sri Venkateswara College (University of Delhi) Dhaula Kuan New Delhi-110021. -- 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
