Re: [gmx-users] -ve value of z in g_wham

Nilesh Dhumal wrote: My box size is 4.5 4.5 4.5 (in nm)90 90 90 Seems awfully large for only 128 waters. I just wonder if the box is distorting during the simulation such that the periodic distance becomes the reference distance, hence the switch between positive and negative distances.

Re: [gmx-users] -ve value of z in g_wham

Nilesh Dhumal wrote: 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. What is the size of the smallest box vector? I ha

Re: [gmx-users] -ve value of z in g_wham

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 pul

Re: [gmx-users] -ve value of z in g_wham

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,

Re: [gmx-users] -ve value of z in g_wham

If I am geting -ve value if z in g_wham then zero is my initial distance or reference distance. 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 comma

Re: [gmx-users] -ve value of z in g_wham

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 sign

[gmx-users] -ve value of z in g_wham

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. Nilesh