Thanks for your replies. :-) So, if I want to the ion move in only z-direction, I need to set the 'pull_dim' Y Y N? Correct?
But in tutorial Justin writes : pull_dim = N N Y: we are pulling only in the z-dimension. Thus, x and y are set to "no" (N) and z is set to "yes" (Y). So what should I do?! Sincerely, Shima ----- Original Message ----- From: Thomas Schlesier <schl...@uni-mainz.de> To: gmx-users@gromacs.org Cc: Sent: Friday, July 12, 2013 9:04 PM Subject: [gmx-users] Re: Umbrella Sampling settings In GROMACS groups are called via the *.ndx file (default: index.ndx) Be aware that 'pull_dim' determines in which diretions (x,y,z) the umbrella potential acts. So use N N Y , if you want that the ion can move freely (onsidering the pull) in the xy-plane and Y Y Y if you want to also restrit the movement in the xy-plane. Am 12.07.2013 17:32, schrieb gmx-users-requ...@gromacs.org: > Allright. > As I said earlier, my system is a lipid bilayer. A channel is inserted in it > and I want to run US on this system. > An ion is considered in center of the each window, the reaction coordinate is > set to z,? so the group which is pulled is an ion, and my ref group would be > COM of the protein. But I don't know what statement is supposed to write in > mdp settings exactly: > ; Pull code > pull??????????? = umbrella > pull_geometry?? = position > pull_dim??????? = N N Y > pull_start????? = yes > pull_ngroups??? = 1 > pull_group0???? = COM of protein > pull_group1???? = ion > pull_init1????? = 0 > pull_rate1????? = 0.0 > pull_k1???????? = 4000????? ; kJ mol^-1 nm^-2 > pull_nstxout??? = 1000????? ; every 2 ps > pull_nstfout??? = 1000????? ; every 2 ps > > > IN fact, to implement such settings, how I make the US understand to get the > COM of protein as the ref group and the proposed ion as the pulled group? > > Would you please give me any suggestions? > > Thanks for all your time and consideration. > > Sincerely, > Shima > > > ----- Original Message ----- > From: Justin Lemkul<jalem...@vt.edu> > To: Discussion list for GROMACS users<gmx-users@gromacs.org> > Cc: > Sent: Friday, July 12, 2013 1:41 AM > Subject: Re: [gmx-users] Umbrella Sampling settings > > > > On 7/11/13 5:10 PM, Shima Arasteh wrote: >> >Thanks for your reply. >> > >> >But when I don't understand why these extra lines are needed to set when >> >are not advantageous practically!:-( >> > > There's nothing "extra."? Everything here has a functional purpose. > > -Justin > >> > >> >Sincerely, >> >Shima >> > >> > >> >----- Original Message ----- >> >From: Justin Lemkul<jalem...@vt.edu> >> >To: Shima Arasteh<shima_arasteh2...@yahoo.com>; Discussion list for GROMACS >> >users<gmx-users@gromacs.org> >> >Cc: >> >Sent: Friday, July 12, 2013 1:37 AM >> >Subject: Re: [gmx-users] Umbrella Sampling settings >> > >> > >> > >> >On 7/11/13 4:21 PM, Shima Arasteh wrote: >>> >>Hi, >>> >> >>> >>I want to run Umbrella Sampling on my system. In initial configurations, >>> >>an ion is located in center of the window. >>> >>Some mdp file settings for running US, as I found in US tutorial are : >>> >>; Pull code >>> >>pull? ? ? ? ? ? = umbrella >>> >>pull_geometry?? = distance >>> >>pull_dim? ? ? ? = N N Y >>> >>pull_start? ? ? = yes >>> >>pull_ngroups? ? = 1 >>> >>pull_group0? ?? = Chain_B >>> >>pull_group1? ?? = Chain_A >>> >>pull_init1? ? ? = 0 >>> >>pull_rate1? ? ? = 0.0 >>> >>pull_k1? ? ? ?? = 4000? ? ? ; kJ mol^-1 nm^-2 >>> >>pull_nstxout? ? = 1000? ? ? ; every 2 ps >>> >>pull_nstfout? ? = 1000? ? ? ; every 2 ps >>> >> >>> >> >>> >>But I'd like to know which lines are specifically for US? Because in this >>> >>step, no group is supposed to be pulled but there are some lines written >>> >>here related to pulling! >>> >> >> > >> >All of them are related to umbrella sampling.? Pulling (steered MD) and >> >umbrella >> >sampling simply use common parts of the "pull code" in Gromacs because US >> >requires a restraint potential.? Whether or not that restraint potential >> >induces >> >net displacement (steering, i.e. non-zero pull_rate) or not (zero pull rate, >> >restrain to a given set of conditions) is the only difference.? Both >> >processes >> >require reference and "pull" groups, geometry information, etc. >> > >> >-Justin >> > -- 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 -- 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
