Re: [gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel

Thomas Piggot wrote: Hi again, Just before I reside myself to rerunning a large number of simulations I was wondering if it is possible to just rerun the simulations where the ion is above and below the reference using pull_geometry=position. Then could I combine these with the other

Re: [gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel

Thomas Piggot wrote: Hi, I am trying to construct a PMF profile for a phosphate ion passing through a membrane protein using umbrella sampling with GROMACS 4.0.5. I have performed the umbrella sampling simulations using the following mdp options and I am now attempting to construct the PMF

Re: [gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel

Jochen thanks for your help. That was what I was afraid of you saying. Oh well, at least this will hopefully provide a useful reference so somebody doesn't make this same mistake. On a side note I noticed a couple of small issues with g_wham. Firstly the -wcorr option says Input, opt. not

Re: [gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel

Thomas Piggot wrote: Jochen thanks for your help. That was what I was afraid of you saying. Oh well, at least this will hopefully provide a useful reference so somebody doesn't make this same mistake. On a side note I noticed a couple of small issues with g_wham. Firstly the -wcorr option

Re: [gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel

Hi again, Just before I reside myself to rerunning a large number of simulations I was wondering if it is possible to just rerun the simulations where the ion is above and below the reference using pull_geometry=position. Then could I combine these with the other simulations where

[gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel

Hi, I am trying to construct a PMF profile for a phosphate ion passing through a membrane protein using umbrella sampling with GROMACS 4.0.5. I have performed the umbrella sampling simulations using the following mdp options and I am now attempting to construct the PMF using g_wham. ; Pull