Selon Tsjerk Wassenaar <[EMAIL PROTECTED]>: > Hi Stephane, > > I think this ends up in treating symptoms. Setting up a simulation of > HIVP should not give such problems. It's probably best to start all > over: pdb2gmx, EM in vacuum, editconf -d 1.0, genbox, EM in solvent, > etc... Keep track of everything you're doing, give all files an > informative name and if you do run into the same trouble, zip up the > log (all command lines given and the output of each program) and all > the files (except .xtc .trr) and make these available through the web. > > Cheers,
And read my post ? Seriously, i'm not a beginner, i'm doing molecular dynamics for years using amber. I'm trying to figure out how precisely i can help others to have an updated procedure for doing a molecular md. My amber experience is probably not good for gromacs since the logic of using files is sometimes different (and it seems heating, equilibration and production is not used often in gromacs, probably due to the fact you can isolate thermal bath for different parts of the system). For the unix/scripting part, i'm sorry, but i don't think there is any problem with this. I even feel the opposite, since a script is reproducible and can lead to the same results all the time, but that's another story. Last, why not looking at my comments and see -> > > > http://www.steletch.org/rpm/gromacs/ Where everything is ... _______________________________________________ gmx-users mailing list gmx-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
