I have a system with 128 water molecules and a ion pair of ionic liquids i.e. one cation and one anion. the reaction corrdination is the distance between cation and anion. Initial distance between cation-anion is 0.8 nm. I have pasted some part of md file
; Pull code pull = umbrella pull_geometry = distance pull_dim = Y Y Y pull_start = NO ; define initial COM distance > 0 ;reftype = com pull_ngroups = 1 pull_group0 = EMI pull_group1 = ETS pull_init1 = 0.0 pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 I run the simulation for 2ns then I run g_wham. I more interested in structure where caion and anion are close ~0.4 nm. After ploting PMF I found that I have -ve value of z. NIlesh On Wed, December 29, 2010 12:51 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> If I am geting -ve value if z in g_wham then zero is my initial >> distance or reference distance. > > That means your pull group has a coordinate that is negative with respect > to the reference group at some point during (at least) one of the umbrella > sampling windows. Zero, in this case, corresponds to an equivalent > coordinate in the pull dimension. > > Without a substantially more detailed description of your system and what > you've done, you're unlikely to get anything more helpful. > > -Justin > > >> Nilesh >> >> >> >> On Sat, December 11, 2010 9:43 pm, Justin A. Lemkul wrote: >> >> >>> Nilesh Dhumal wrote: >>> >>> >>>> Hello, >>>> I trying to run umbrella sampling simulation for system. >>>> >>>> >>>> >>>> After running g_wham command I am geting some negative value of z >>>> along x axis. >>>> >>>> g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kcal >>>> >>>> Can any one tell why I am geting -ve value or what is the >>>> significance of this. >>>> >>> That means the coordinate of your pull group is less than that of >>> your reference group along the reaction coordinate. The reason for >>> that depends on how you constructed your pull and reference groups and >>> how you carried out the umbrella sampling. >>> >>> -Justin >>> >>> >>> >>>> Nilesh >>>> >>>> >>>> >>>> >>>> >>>> >>> -- >>> ======================================== >>> >>> >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/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 >>> >>> >>> >>> >> >> >> > > -- > ======================================== > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/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
