Re: Re: [Fwd: [gmx-users] preferred/best force fields]

Dear Mark, Thanks for your input. Maybe it does not fit exactly what I would like (should there be what I would like), but it brings me worthy information to clear my vision on how I might carry this on. Yours, Jorge iu...@interponta.com.br wrote: Hi, I see there are many inte

[Fwd: [gmx-users] preferred/best force fields]

Hi, I see there are many interesting topics going on, maybe due to this I did not receive any answer/suggestion/comment to my question or maybe it is rather naive. Anyway, it would like to listen to the experts if there are no other suggestions to add to what I did below. Thanks,

[gmx-users] preferred/best force fields

Dear All, I am new to molecular dynamics, had some tutorials and could run some initial tests successfully in that they finished without errors (now to analyze if results make sense). Now my challenge is to make a molecular dynamics of a homohexamer which binds to a ssDNS and a co-f

Re: Re: [gmx-users] genbox error at futil.c

es the old one according to the conventions (which in my script I could then further "re-rename"). And... genbox does need a previous topology file (RecA_nat_b4em.top was intended to be the output file!). Thanks, again. Jorge iulek wrote: Hi! I am a very beginner,

[gmx-users] genbox error at futil.c

Hi!     I am a very beginner, trying to make some dynamics of a protein in a water box, after doing some (web) tutorials. I googled first for this (possibly simple) error, found one reference, but cannot see it, possibly because the gromacs site is under changes.     I ran pdb2gmx and editconf