Re: [gmx-users] PROTEIN FOLDING

Depends. If you're interested in local folding and there are SS motifs in the region you're interested, then yes. If not, no. In terms of overall folding of the entire protein, yes it surely can be an important analysis. J On Wed, Dec 20, 2017 at 1:46 PM, Neha Gupta

Re: [gmx-users] PROTEIN FOLDING

Thank you Joao and Aman. I have noted the points you have suggested. Do you think analyzing DSSP would help? Thanks, Neha On Wed, Dec 20, 2017 at 4:03 PM, João Henriques < joao.m.a.henriq...@gmail.com> wrote: > "You can use various supporting tools from R language to debug your > trajectory

Re: [gmx-users] Dynamic selection of a shell in a trajectory

Hi, Dynamic selections are implemented, but only for a small subset of GROMACS tools. You can use gmx select to form the appropriate index group, but you'd have to write some other script to get trjconv to pull out individual frames with the matching selection, and then concatenate them into a

Re: [gmx-users] PROTEIN FOLDING

"You can use various supporting tools from R language to debug your trajectory but most third party software support NAMD and charmm format. You can use VMD to convert the trajectory to dcd and use R language based packages to read your trajectory" What? How is this useful or helpful? At most it

Re: [gmx-users] Grompp error : Incorrect number of parameters

Hi, The large energy means your topology is probably broken. Please use a tool that will write an .itp file for you (e.g. SwissParam?), or next time get your topology for your ligand working before you try to use it in a complex. Even get a simple form of the ligand working first, to teach

Re: [gmx-users] Measuring distance to the nearest image

Hi, From its help: "gmx distance calculates distances between pairs of positions as a function of time. Each selection specifies an independent set of distances to calculate. Each selection should consist of pairs of positions, and the distances are computed between positions 1-2, 3-4, etc."

Re: [gmx-users] Dynamic selection of a shell in a trajectory

Very unlikely and/or impractical. The water selections/analyses you can do with gromacs' native tools are unfortunately rather limited. From personal experience I'd suggest trying MDAnalysis or something similar, because it gives you the freedom to code your our analysis routine with minimal

Re: [gmx-users] Grompp error : Incorrect number of parameters

To be included here, the ligand I have uploaded seems to be so congested and out of form. Look literally like a clumsy ball. I am not sure what make this happen. On Wed, Dec 20, 2017 at 2:51 PM, RAHUL SURESH wrote: > Dear Alex > > I have tried that but the system

Re: [gmx-users] Grompp error : Incorrect number of parameters

Dear Alex I have tried that but the system collapse. For em_real.mdp option,I get message stating Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). It stopped because the algorithm tried to make

Re: [gmx-users] Measuring distance to the nearest image

Hi Mark, I think with a combined project list as long as my arm and going between VMD and Gromacs that the fault lies with me. A misunderstanding with the decimal point. However, I am a little confused over the output and despite reading the help I am still none the wiser. I go on to select

Re: [gmx-users] Grompp error : Incorrect number of parameters

The description for the Urey-Bradley potential (assuming two quadratic terms qualify for the proud term "potential") is described in the user manual, and the constants' order of appearance in the itp file is given in the Table 5.5 of the manual. If you have a basic quadratic angular term

[gmx-users] Dynamic selection of a shell in a trajectory

Dear all, I'm performing a dynamic of a metal ion in a box consisting of a solvent, where the metal is coordinated by six solvent molecules. I'm writing here because I want to reduce the trajectory including the intire box to a trajectory containing only the first coordination shell of the