Re: [gmx-users] Test particle insertion change in energy - group cut off scheme

I see. Thank you. I understand how tpi in gromacs works now. Perhaps my last question. Is there a restriction on the number of charge groups in gromacs ?. For example can it be equal to the number of atoms in the system ? How do think it will affect the performance of tpi which uses the group

Re: [gmx-users] Test particle insertion change in energy - group cut off scheme

Hi, Please see the reference manual for details, but the charge groups are defined in the topology however you wish (and need not have a net charge). Mark On Sun, Mar 4, 2018, 00:18 Arun Srikanth wrote: > Thank you. > > Can you please elaborate on this or clarify the

Re: [gmx-users] Test particle insertion change in energy - group cut off scheme

Thank you. Can you please elaborate on this or clarify the following questions? 1. Supposing I have inserted one water molecule inside a polymer (an interconnected network with net zero charge), the electrostatic interactions should be computed between every atom of water and polymer atoms

Re: [gmx-users] Test particle insertion change in energy - group cut off scheme

Hi, TPI will only work if you choose the group cutoff scheme. But the impact of that difference is nearly zero. Mark On Sat, Mar 3, 2018, 22:29 Arun Srikanth wrote: > Hello all > > I was going through tpi.cpp file in the latest version of gromacs. > > I found this flag >

[gmx-users] Test particle insertion change in energy - group cut off scheme

Hello all I was going through tpi.cpp file in the latest version of gromacs. I found this flag "TPI does not work (yet) with the Verlet cut-off scheme" My question: Does test particle insertion use the group cut off scheme to calculate the change in energy ? (assuming equilibrium trajectories

Re: [gmx-users] Umbrella sampling

On 3/3/18 9:27 AM, rose rahmani wrote: Sorry, i can't understand, what do you mean"-zprof0" option? Could you please give me an example? Please read the gmx wham help information for a description. -Justin On 3 Mar 2018 16:47, "Justin Lemkul" wrote: On 3/3/18 7:02 AM,

Re: [gmx-users] Umbrella sampling

Sorry, i can't understand, what do you mean"-zprof0" option? Could you please give me an example? On 3 Mar 2018 16:47, "Justin Lemkul" wrote: On 3/3/18 7:02 AM, rose rahmani wrote: > Hi > > I use umbrella sampling to calculate PMF, for studying the interaction of > different

[gmx-users] Cluster analysis on molecules

Hi all, I want to calculate the number of clusters of my glycine molecules during the course of my simulation. I have read that gmx clustsize is the correct command to use. I read on one of the previous threads that I will have to create a separate tpr file for the molecules of interest. I

Re: [gmx-users] Umbrella sampling

On 3/3/18 7:02 AM, rose rahmani wrote: Hi I use umbrella sampling to calculate PMF, for studying the interaction of different aminoacids with nanosheet separately. But at the minimum distance from sheet, potential is zero for all PMF diagrams. I mean there isn't any positive potential even at

[gmx-users] Umbrella sampling

Hi I use umbrella sampling to calculate PMF, for studying the interaction of different aminoacids with nanosheet separately. But at the minimum distance from sheet, potential is zero for all PMF diagrams. I mean there isn't any positive potential even at closest distance of aminoacid from sheet.