[gmx-users] npt equilibration nanotubes

Hello, For those who have simulated with nanotubes, how have you performed an nPT equilibration of your systems. I have used a freeze group on my nanotube, however, I know this is incompatible for pressure coupling. Thanks, Anand -- Gromacs Users mailing list * Please search the archive at htt

[gmx-users] Buckingham Potentials and oplsaa

Hi all, Thanks for the advice in advance. I want to simulate a titania nanotube with a biomolecule using parameters described previously by Matsui-Akaogi (1991) for titania. How do I add parameters for the buckingham potential for my titanium and oxygen atoms? Thanks, Anand -- Gromacs Users mail

[gmx-users] Volume and boundary Questions

Hello, I have two questions about setting up my box for simulation. Thank you for any and all input in advance. 1. Is the simulation box dimensions and volume fixed throughout the simulation (or are they allowed to fluctuate around the set dimensions)? 2. Is it possible to make custom box shapes

Re: [gmx-users] Beginner Question -- Grab Info from Output

ues of interest, you can use a gazillion > different approaches. grep and/or awk would be good choices, but you don't > seem very confident with the terminal, so I guess it's better to stick with > a text editor. > > Best regards, > J > > > On Thu, Mar 10

[gmx-users] How to Set Boundary in Gromacs

Hello, I want to create many nanotubes periodically by extending one hexagonal tube in three dimensions. I am wondering if it is possible, or necessary, to set boundaries in Gromacs. In NAMD we can input the boundary for periodicity as a .bound file and set the periodicity to xyz using the bound f

[gmx-users] Beginner Question -- Grab Info from Output

Hi, I am running gmx msd and would like to import the value of the calculated diffusion coefficient and error that is output in my linux terminal. I know I can view the trajectory with grace or parse the file in a text editor for its values, but I would just like end calculation. Is there a way I

[gmx-users] protein transport in nanotube

Hi, Is there any tutorial or available code for simulation of an arbitrary protein transport in a nanotube. I would like to learn how this approach and model/implement this for obtaining diffusion coefficients. Thanks -- Gromacs Users mailing list * Please search the archive at http://www.grom

[gmx-users] Dynamic Cross Correlation

Hello, Is there any method in GROMACS to compute dynamic cross correlation between different molecules. If not defined in GROMACS, what are methods people take to compute coupling from the trajectory data. Thanks, Anand Dharia -- Gromacs Users mailing list * Please search the archive at http:/

[gmx-users] Clustering of Molecules Gromacs

Hello, I am wondering if there is any built-in method that Gromacs may have to quantify the extent of clustering between protein molecules. Thanks, Anand Dharia -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posti

[gmx-users] (no subject)

Hello, How can I restrain the position of one group of molecules, but let them interact with other molecules free to move within the system? Thanks, Anand Dharia -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before post

Re: [gmx-users] Non Periodic Coordinate File

Wow, thank you so much, don't know how I didn't realize this. On Thu, Aug 20, 2015 at 3:01 PM, Justin Lemkul wrote: > > > On 8/20/15 5:59 PM, ANAND AMITKUMAR Dharia wrote: > >> Hello, >> >> I was wondering if it was possible to create a non-periodic coo

[gmx-users] Non Periodic Coordinate File

Hello, I was wondering if it was possible to create a non-periodic coordinate file using trjconv or some other gromacs program on a trajectory file. I would like to use coordinate data to calculate displacement in order to compute a crosscorrelation between molecules, however, with the jumps in th

[gmx-users] Hard Wall Boundary

I understand the solver is more straightforward with the periodic boundary condition. However, I want to know if it is possible to implement hard wall boundaries to restrict the protein motion. This will be much more representative of our model than the periodic approach we have been currently usin

Re: [gmx-users] Inorganic Material Simulations

Thanks for your quick response. We are thinking about using input parameters from experimental data as a first approach. Is there documentation on the syntax for the input files that we may be able to use to get a better idea. I had downloaded a .itp file for a drude oscillator, but was unsure of t

[gmx-users] Inorganic Material Simulations

Hey there, I am interested in simulating a protein diffusing inside an inorganic nanotube. I want to study how the diffusivity of the protein changes as a results of the surface interaction with the nanotube. Specifically, I am looking to understand how to define a force field for the nanotube and