Re: [gmx-users] How to Calculate tetrahedral order parameter

Den 2019-09-03 kl. 14:02, skrev Soham Sarkar: Sorry, I forgot to mention that I have two systems. One consists of protein-water and the other one consists of protein-water-urea. I need to calculate the tetrahedral order parameter of water around the protein within 0.4nm for these two systems.

Re: [gmx-users] How to Calculate tetrahedral order parameter

Sorry, I forgot to mention that I have two systems. One consists of protein-water and the other one consists of protein-water-urea. I need to calculate the tetrahedral order parameter of water around the protein within 0.4nm for these two systems. Thanks and regards- Soham On Tue, 3 Sep 2019,

Re: [gmx-users] How to Calculate tetrahedral order parameter

Den 2019-09-03 kl. 13:26, skrev Soham Sarkar: Dear all, I know this question was asked by many users before but searching them all I did not get how to perform it in GROMACS. Please help me with this. Is there any in built command line exist for Tetrahedral order parameter calculation?

[gmx-users] How to Calculate tetrahedral order parameter

Dear all, I know this question was asked by many users before but searching them all I did not get how to perform it in GROMACS. Please help me with this. Is there any in built command line exist for Tetrahedral order parameter calculation? If gmx hydorder is the existing tool for

Re: [gmx-users] How to calculate tetrahedral order parameter in GROMACS

Thanks. I am checking. On Wed, 8 May 2019, 2:30 pm David van der Spoel, wrote: > Den 2019-05-07 kl. 14:34, skrev Soham Sarkar: > > Hello, > >I have two systems. One containing only water and the other one > > contains protein and water. Using g_select I made water in 1st solvation > >

Re: [gmx-users] How to calculate tetrahedral order parameter in GROMACS

Den 2019-05-07 kl. 14:34, skrev Soham Sarkar: Hello, I have two systems. One containing only water and the other one contains protein and water. Using g_select I made water in 1st solvation shell but the use of g_hydorder I cannot understand. I read the disscussion so far disscussed. For

[gmx-users] How to calculate tetrahedral order parameter in GROMACS

Hello, I have two systems. One containing only water and the other one contains protein and water. Using g_select I made water in 1st solvation shell but the use of g_hydorder I cannot understand. I read the disscussion so far disscussed. For these two systems which index I need to choose,

[gmx-users] How to calculate tetrahedral order parameter?

Dear gromacs users, Hello. I am working on bulk water system simulation. I am trying to calculate tetrahedral order parameters in gromacs by using "gmx hydorder" command. Dose anyone know how to process outputs generated by "hydorder" command? It is in the form of output.xpm file. Thanks in