RE: [gmx-users] REMD question
Michael, Thank you for your answer. On the other hand, I´m not implementing, I´m using REMD.. I miss wrote it. Nathalia -Mensaje original- De: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] En nombre de Michael Shirts Enviado el: lunes, 28 de mayo de 2012 08:09 p.m. Para: Discussion list for GROMACS users Asunto: Re: [gmx-users] REMD question Gromacs already supports replica exchange -- what particularly are you implementing? Equilibration of pressure is always a good idea -- even if you are running NVT simulations, you want to get them to be at the equilibrium volume for your system and temperature choice, which will require equilibration at constant pressure. On Mon, May 28, 2012 at 4:37 PM, Nathalia Garces wrote: > Dear Gromacs Users, > > > > We are implementing REMD method in Gromacs in protein folding, in your > web page you give some steps that don´t mention any step about NPT > stabilization. This step is necessary to run REMD simulations? > > > > Thank you in advance, > > > > Nathalia > > > > > -- > gmx-users mailing list gmx-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] REMD question
Dear Gromacs Users, We are implementing REMD method in Gromacs in protein folding, in your web page you give some steps that don´t mention any step about NPT stabilization. This step is necessary to run REMD simulations? Thank you in advance, Nathalia -- 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] analysis pdb file
Good Day, I ran a molecular dynamic simulation for over a month and I gathered the ".pdb" file containing the molecular structure at the end of the simulation. I can see the final configuration using a pdb viewer but I would like to know if it is possible (without redoing the simulation) to obtain previous configurations of the atoms. Thank you for your help, Nathalia -- 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] using gromacs with an specific GCC
Good morning, I'm trying to use Scientific Linux 5.5 to run Gromacs 4.5.4. The problem is that the default version of gcc in this distribution is 4.1, which is broken for Gromacs!! I can install a newer version of gcc in compatible mode with gcc 4.1, but the last one will still be the default. Now, my problem is that I don't know how to specify to Gromacs to use the newer version. I've seen that you can specify which gcc to use while you configure the program, but I found no information of how to specify which compiler to use while running a MD simulation??.. I mean when using mdrun command or even while using every command in Gromacs. Thank you for four answer Nathalia -- 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] Installation gromacs in Scientific Linux
Hello, The last 6 months I've been working with gromacs (4.5.3 and 4.5.4) in Ubuntu (10.4) and it has worked fine. The problem started when I changed the linux distribution to Scientific Linux (5.3)... I followed the same steps to download/configure gromacs but something's wrong or missing because the simulations that I had been running on UBUNTU crashed in SL. The command I use is very simple: * mdrun -v -s topol.tpr* In Ubuntu the simulation ends fine but in SL the application starts to write on prompt at early steps (around 100) *Step XX, time 0.XX (ps) LINCS WARNING* *relative constraint deviation after LINCS:* *rms XX, max XX (between atoms XX and XX)* *bonds that rotated more than 30 degrees:* *...* *Wrote pdb files with previous and current coordinates* * * Until the simulation ends (around 250) with a message of * Segmentation fault * I tried different ways to configure gromacs but none of them seems to resolve the problem 1) ./configure --prefix= make make install 2) ./configure --with-fft=fftw3 --prefix= --without-x make make install 3)./configure --program-suffix= --disable-float --prefix= --exec-prefix= --enable-all-static --with-fft=fftw3 --without-x make make install Moreover, I downloaded the benchmark posted in the gromacs web page to test the simulations with other ".tpr" files. I run the first simulation (implicit solvent) in UBUNTU and worked OK but the one on SL crashed (around step 460) with the first two options of configuration. The last configuration enabled the simulation to run OK( I decided to stop it at 4000 steps)... This bewilders me because the last configuration permitted the benchmark to run OK but not my file. I don't think my file has an unstable system because it works all right in UBUNTU (and also Debian!) In addition, I upgraded my linux distribution to the latest SL 5.x release but it didn't make any change! I hope you can help me with some guide on how to proceed a GOOD instalation in SL or to let me know what is my problem and what I am missing. Thank you for four answer, Nathalia Garces -- 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] mdrun-gpu
Hello, I want to know if it is possible to use "mdrun-gpu" with the command "-multi", meaning to use GPUs using paralell simulation. When I used it (mdrun-gpu -multi 2 -replex 2 ), it appears me an error shown bellow * Fatal error: This binary is compiled without MPI support, can not do multiple simulations.* this bewilder me because I'm not sure I can use gpu and mpi at the same time. Thank you for four answer Nathalia -- 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
