-------- Original-Nachricht -------- > Datum: Wed, 18 Apr 2012 03:13:09 +1000 > Von: Mark Abraham <mark.abra...@anu.edu.au> > An: Discussion list for GROMACS users <gmx-users@gromacs.org> > Betreff: Re: [gmx-users] Re: Questions
> On 18/04/2012 12:10 AM, lloyd riggs wrote: > > Included below (although Im terrified youll invalidate massive parallel > work with a single comment) is the .mdp file I used for 10 of the runs, > basically it was the only way I could get it to run. The time step is small > because of the small molecule involved, however I painstakingly looked up all > parameters ten times. Basically its only violation was with links, which > seems to think S-O---H isnt supposed to roatate so much, but the molecules > degrees of freedom (1/2 can rotate 360 from the other along a central axis) > etc... > > > > PR p-coupling is poor for stability during equilibration (since gen_vel > = yes), and it's always poor to start your production run (i.e. your > pulling) without prior equilibration. Equilibrate with berendsen, then > switch to PR for a bit and only then worry about pulling. I had woundered as I always have to throw out the first 2 picosecounds about the init velocity. I did equilibrate each first untill there was no change with bereendsen and nose-hoover, so from my mistake thats what I have had to do for the data. Is there any other critiques, as I COULD USE THEM. Aside, I have a wierd problem where WHAM reads 1 file then not the next. Then, I use as mentioned a text editor and it reads 2 different files for input, but not the others that had worked. I cant figure out why it reads one say with tabs spacing, and the next with 2 bar spaces, and the next with only bar space 1? In the end I can find one or two differences in emacs or editors, but then the final .xvg files all have different spacing as above and then I cant read all of them in to get the proper weighted scores? Thanks Stephan > > Mark > -- > 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 -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a -- 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
