[gmx-users] how to calculate kinetic constant?

Hello: I've submit a simulation in gromacs, and I am just wondering how can we calculate kinetic constant for the ligand bound/ubound process? thanks a lot Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the

[gmx-users] OPLS/AA + TIP5P, anybody?

Dear Grzegorz: From a quick look at your .mdp, I also suggest that you go back to your system including the peptide that you had managed to finish EM with modified flexible tip5p but then crashed with the standard rigid tip5p during MD and try the MD again using gen-vel = yes if you're still

[gmx-users] Membrane is shifted a lot during umbrella sampling

Dear Sudipta: on average, bilayers migrate along the positive z axis during gromacs simulations with a variety of atomistic force fields. This has been reported before, but never fully resolved ( http://redmine.gromacs.org/issues/165 suggests it is due to rounding ) and I see it all the time.

Re: [gmx-users] how to calculate kinetic constant?

On 2013-10-04 12:30, Albert wrote: Hello: I've submit a simulation in gromacs, and I am just wondering how can we calculate kinetic constant for the ligand bound/ubound process? thanks a lot Albert Check out our recent paper and references therein:

[gmx-users] Verlett buffer drift

Hi all I am running a MD simulation using GPU version of GROMACS 4.6 and I am asked to use Verlett cut-off scheme.  I am new to GPU computing and I did not find much information about the scheme in the manual. I would very thankful if anyone who has used the Verlett scheme can let me know

[gmx-users] pull-code constant-force direction gives unexpected error about distance larger than box size

Dear Users: I am trying to use the pull code to add a constant force in a particular direction. I am getting an error that the initial distance is greater than 1/2 the box size. (error in 4.5.5, 4.6.1, 4.6.3) I must not understand how to use this. I checked the online .mdp options:

[gmx-users] What are F1~F4 of Equation(4.63) of Gromacs manual-4.5.6

Hi, My name is Insung Na. I want to introduce certain dihedral's Ryckaert-Bellemans coefficients to OPLS-AA ffbonded.itp file. For calculation, I found information on that from Gromacs manual-4.5.6 At equation 4.63, the formula contains F1, F2, F3, and F4. It seemed that I need those values to

Re: [gmx-users] Membrane is shifted a lot during umbrella sampling

On 10/4/13 10:32 AM, Christopher Neale wrote: Dear Sudipta: on average, bilayers migrate along the positive z axis during gromacs simulations with a variety of atomistic force fields. This has been reported before, but never fully resolved ( http://redmine.gromacs.org/issues/165 suggests it