Re: [gmx-users] Umbrella sampling-gmx distance

Oops,Sorrry. Sometimes big challenges make ones think hard and ignore obvious issues. Thank you so much Mr.justin and joao On Sat, Jan 13, 2018 at 4:01 PM, João Henriques < joao.m.a.henriq...@gmail.com> wrote: > The output is very explicitly telling you what the problem is. You didn't > provide

Re: [gmx-users] Umbrella sampling-gmx distance

The output is very explicitly telling you what the problem is. You didn't provide a topology. Pass one the the -s flag. How do you want the COM to be computed when you're not providing any masses? J On Jan 13, 2018 9:19 AM, "rose rahmani" wrote: > I'm relly sorry for

Re: [gmx-users] Umbrella sampling-gmx distance

I'm relly sorry for asking you again and again but... GROMACS: gmx distance, VERSION 5.1.4 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Command line: gmx distance -n index.ndx -f conf0.gro -select 'com of group 2 plus com of group 6'

Re: [gmx-users] Umbrella sampling-gmx distance

On 1/11/18 11:38 AM, rose rahmani wrote: [ ZnS ] 123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45..

[gmx-users] Umbrella sampling-gmx distance

[ ZnS ] 123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45.. [ Protein ] 761 762 763 764 765 766 767

Re: [gmx-users] Umbrella Sampling-gmx distance

On 1/11/18 9:50 AM, rose rahmani wrote: still like this You're not using the command syntax shown in the link I provided. -Justin # This file was created Thu Jan 11 09:46:46 2018 # Created by: # :-) GROMACS - gmx distance, VERSION 5.1.4 (-: # # Executable:

Re: [gmx-users] Umbrella Sampling-gmx distance

still like this # This file was created Thu Jan 11 09:46:46 2018 # Created by: # :-) GROMACS - gmx distance, VERSION 5.1.4 (-: # # Executable: /usr/local/gromacs/bin/gmx # Data prefix: /usr/local/gromacs # Command line: # gmx distance -n index.ndx -f conf0.gro -oxyz dist0.xvg

Re: [gmx-users] Umbrella Sampling-gmx distance

On 1/11/18 3:43 AM, rose rahmani wrote: Hi i'm doing umbella sampling. whenever i use gmx distance after pulling in V.5.1.4 , i wouldn't have proper dist.xvg file.for example; this my mdp file for pulling: integrator = md dt = 0.001 nsteps

[gmx-users] Umbrella Sampling-gmx distance

Hi i'm doing umbella sampling. whenever i use gmx distance after pulling in V.5.1.4 , i wouldn't have proper dist.xvg file.for example; this my mdp file for pulling: integrator = md dt = 0.001 nsteps = 250 nstxout = 5000