[gmx-users] G_hbond and periodicity

Hi all, Does periodic boundary affect the calculation of hydrogen bond if my protein is not in one box? What about other calculations? Thank you, Tang jiaowei ___ gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] ffamber updates

Hi Eric Thanks for doing that great job concerning the amberFF for GROMACS. I recently came across this paper: http://www.biophysj.org/cgi/content/abstract/92/11/3817?maxtoshow=HITS=10hits=10RESULTFORMAT=searchid=1FIRSTINDEX=0volume=92firstpage=3817resourcetype=HWCIT There Perez et al refined

[gmx-users] fatal error in nsgrid

I've been running on 16 processors a protein MD simulation. During the simulation I've got a crash and the standard error reported this: Fatal error: ci = 10280 should be in 0 .. 10050 [FILE nsgrid.c, LINE 218] [0] MPI Abort by user Aborting program ! [0] Aborting program! What could that be?

Re: [gmx-users] G_hbond and periodicity

Hi Tang Jiaowei, g_hbond takes periodicity into account, like most tools do. Do note that this doesn't work if you've performed rotational transformations (lsq-fitting). Cheers, Tsjerk On 9/28/07, tangxuan [EMAIL PROTECTED] wrote: Hi all, Does periodic boundary affect the calculation of

Re: [gmx-users] gromacs result

Right, but I can just warn anyone. Trying to use TI on a docked structure is insanity... The docked structure is an approximation in its best case (more likely its simply crap). Applying a free energy calculation towards such a structure will give you everything...but sure not the the correct

Re: [gmx-users] gromacs result

Maik Goette wrote: Right, but I can just warn anyone. Trying to use TI on a docked structure is insanity... The docked structure is an approximation in its best case (more likely its simply crap). Applying a free energy calculation towards such a structure will give you everything...but sure

Re: [gmx-users] ffamber updates

Hi Maik, These updated NA params would be nice to add and test, but I've been too busy lately to do this. I'd like to get to it soon though (i.e. this year ;o) As for AMBER-99SB, the paper makes reasonable arguments I think, but I've not run any real test or production runs with 99SB

[gmx-users] Reading XTC files from fortran90

Hi all. I'm writing this beucase I'm having terrible problems in trying to deal with gromacs trajectory files with my own programs, originally written on fortran90. The codes themselves are enoughly big to make it out of question to try to translate them. What leads to some sort of mixed

Re: [gmx-users] Reading XTC files from fortran90

Hi, try: download http://www.mpibpc.gwdg.de/groups/de_groot/xtc.tar.gz (and optionally issue a 'make' in the xtc directory after unpacking) in the linking stage, use something like ifort -blabla -lxdrf -L/wherever/xtc -lg2c your smalll test code looks OK apart from the fact that I don't know