[gmx-users] Umbrella sampling question

Can you please let us know exactly how you got the two values that you find to be different (but expected to be the same)? i.e. post your full g_dist command and explain how you observed the value in the output from mdrun. One frame should be enough for now (as long as you are sure -- and can pr

Re: [gmx-users] Umbrella sampling question

Hi Chris, Thank you very much for your reply. I will give you more details on my US. Initially ligand is positioned at the starting of the channel and pulled down wards.(SMD) 1. I have generated all configurations from the SMD(trjconv). 2. Created one index group for center of the channel and ano

[gmx-users] Umbrella sampling question

Aswathy: We can't tell if you did US correctly unless you post what you have done. You must give more info and you must copy and paste the actual input / .mdp parameters that you used. As for if your PMF is correct, then we can never tell you that. You can, however, ensure that your sampl

[gmx-users] Umbrella sampling question

Hi Gromacs users, Let me give an idea about what i am doing. I was doing a Steered Molecular dynamics of ligand transport through the transporter channel. I want to do the PMF calculation using Umbrella sampling. I followed the steps provided in the (Justin's) tutorial. I have generated all configu