[gmx-users] inconsistent shifts while using distance restraints

Dear gmx-useres, I am simulating a protein in a box with water and ions and now I am trying to keep the ions away from a particular residue of the protein. To do this I am using distance restraints. So I created a new molecule type with the protein and all ions and added distance restraints

[gmx-users] strange behaviout in 5.1.2

Dear All, when using gmx-5.1.2 with a mdp file with the following pressure coupling parameters: ; pressure coupling Pcoupl = berendsen Pcoupltype = semiisotropic nstpcouple = -1 ; Time constant (ps), compressibility (1/bar) and reference P (bar)

[gmx-users] Regression test for mdrun only installation

Dear GMX-Users, just one quick question: is there a simple way to do the regression test with a mdrun-only build of gromacs 5.05? cheers, Daniel

[gmx-users] g_wham error in umbrella simulation

Maybe some empty lines at the end of your .dat files. Dear all, I am doing an umbrella simulation, and come across the following error. Command line: g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000 Found 27 tpr and 27 pull force files in tpr-files.dat and

[gmx-users] Variable force constant in umbrella sampling

Dear gromacs users, I have again some question regarding umbrella sampling. Is it ok to use different force constants in the different umbrella runs? So far I only read papers where they keep it constant but for me it could be useful to vary this along the reactioncoordinate. Best, Daniel

Re: [gmx-users] Variable force constant in umbrella sampling

. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Kortzak, Daniel d.kort...@fz-juelich.de Sent: 12 February 2015 22:58 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Variable force constant in umbrella

[gmx-users] Free energy calculations with pull code and umbrella sampling

of those frames instead of pulling the whole way from the binding site to the bulk. On 2/5/15 6:59 AM, Kortzak, Daniel wrote: Dear All, I want to calculate the free energy of binding of a single sodium ion to a protein. I want to do this by decoupling the ion in the binding site

Re: [gmx-users] Position restraints and free energy calculations

Wouldn't just using the pull code to do umbrella sampling be a much more straightforward approach? You don't have to deal with compensating for artifacts associated with the restraint potential during decoupling and removing a charge from the system. -Justin Hi Justin, thanks for your fast

[gmx-users] Position restraints and free energy calculations

Dear All, I want to calculate the free energy of binding of a single sodium ion to a protein. I want to do this by decoupling the ion in the binding site (with the couple-moltype approach). The work-flow I have in mind is roughly: 1. Start with ion in binding site 2. Turn on position