[gmx-users] How to find free energy barriers between conformational sub-states of simulation?

Dear gromacs users, I have done simulations of 20 residue length peptide for 100ns. I have performed clustering and got some 29 clusters. Now would like to calculate the free energy difference between these clusters. kindly tell me how to find the free energy difference between the clusters.

[gmx-users] strange behavior during energy minimization

Dear Gromacs users, I get strange behavior when trying to energy minimize a frame from a simulation. I'm probably overlooking some settings, but I would appreciate any advice. I have a membrane protein system prepared using CHARMM-GUI of about 80k atoms (CHARMM36 ff, TIP3 water). I'm using

[gmx-users] sampling convergence of FEL

Dear users, I have a 100 ns simulation trajectory and I have generated FEL (free energy landscape) with it to extract a minimum energy conformation of my protein. How can I show sampling convergence of FEL in gromacs? Do I have to split the trajectory (say 50:50) and generate FELs from both

Re: [gmx-users] How the pH is reflected in Gromacs?

Based on your pKa prediction by PDB2PQR, set protonation state for Asp/Glu/His/Lys/Arg accordingly. That is all you can do in GROMACS. Constant pH MD should be used if you want to make your simulation pH responsive. Cheers On Wed, May 17, 2017 at 11:18 AM, ZHANG Cheng <272699...@qq.com> wrote:

[gmx-users] How the pH is reflected in Gromacs?

Dear Gromacs,I am simulating pH 4 condition. I interactively assign the protonation of chargeable residues of a protein based on PDB2PQR results by setting pH=4 in the "pKa Options" (http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/). I do not add citrate or acetate molecules to the simulation box. So

Re: [gmx-users] ligand moving out during umbrella sampling

This time I think I got ligand restrained successfully during the umbrella sampling. I have removed the restrain from protein, as per your advice. Defined the COM vector in md_umbrella.mdp, applied pull_k1=1000 and used pull_rate1=0.0. I have uploaded the trajectory movie (and other mdp files) in

Re: [gmx-users] Amber03ws includes an unexpected dihedral with atoms -C N CA CB

On 5/17/17 6:04 AM, Ramon Crehuet wrote: Dear all, I would like to use the Amber03ws force field described in Best, Zheng and Mittal, J. Chem. Theor. Comput., 10, 5113-5124, 2014. This force field is contributed in http://www.gromacs.org/Downloads/User_contributions/Force_fields When using

Re: [gmx-users] Problem setting up SMD simulation for DNA

On 5/17/17 6:35 AM, Nicholus Bhattacharjee wrote: Hello user, I am trying to setup SMD simulation for a DNA. I am following the tutorial from Bevanlab where SMD was on protein performed to use as input for umbrella sampling.

Re: [gmx-users] md continuation

see command gmx convert-tpr On Wed, May 17, 2017 at 3:22 PM, Kashif wrote: > I have already run my 20 ns md simulation of my protein. The log file is > showing completion of my 20 ns data. I have also done analysis by using > trjconv command and g_rms. > Now I want

Re: [gmx-users] md continuation

Hi, You need a new .tpr with a larger number of steps, by using the -extend option of whichever tool (tpbconv or gmx convert-tpr) is in the GROMACS version you're using (which is a really useful thing to mention when asking for help...) Mark On Wed, May 17, 2017 at 11:53 AM Kashif

Re: [gmx-users] NMA eigenvectors doubts

On Wed, May 17, 2017 at 11:15 AM luca maggi wrote: > Hi Mark, > > Thanks..But Even if I didn't minimized very well my system I can't > understand why the calculation of the hessian is performed just on some of > the total DoF. It is probably an issue of memory allocation.

[gmx-users] Problem setting up SMD simulation for DNA

Hello user, I am trying to setup SMD simulation for a DNA. I am following the tutorial from Bevanlab where SMD was on protein performed to use as input for umbrella sampling. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html Now for initial setup I am

Re: [gmx-users] symmetrical LJ binary mixture simulation

Hi, There's no way to implement that. I suggest you consider alternative ways of inducing phase separation that is achieved with parameters that follow geometric combination rules. Mark On Wed, May 17, 2017 at 11:40 AM Hyuntae Jung wrote: > Dear Mark Abraham, > > > Sorry for

[gmx-users] Amber03ws includes an unexpected dihedral with atoms -C N CA CB

Dear all, I would like to use the Amber03ws force field described in Best, Zheng and Mittal, J. Chem. Theor. Comput., 10, 5113-5124, 2014. This force field is contributed in http://www.gromacs.org/Downloads/User_contributions/Force_fields When using it, Gromacs reports a warning about a CB

[gmx-users] md continuation

I have already run my 20 ns md simulation of my protein. The log file is showing completion of my 20 ns data. I have also done analysis by using trjconv command and g_rms. Now I want to increase my simulation at least for 20 ns more and make my data of protein simulation for 40 ns. Kindly help for

Re: [gmx-users] symmetrical LJ binary mixture simulation

Dear Mark Abraham, Sorry for frustrating this, I was supposed to explain the Lennard Jones (6-12) potential form for Van der Waals interaction. In other words, I consider the binary system with two spheres (A and B) which interact only Van der Waals interaction with 6-12 potential form,

Re: [gmx-users] NMA eigenvectors doubts

Hi Mark, Thanks..But Even if I didn't minimized very well my system I can't understand why the calculation of the hessian is performed just on some of the total DoF. It is probably an issue of memory allocation. Indeed performing the same calculation just on the protein (bad minimized

Re: [gmx-users] symmetrical LJ binary mixture simulation

Hi, On Wed, May 17, 2017 at 5:29 AM Hyuntae Jung wrote: > Hello, gromacs users. > > > I wonder if it is possible to simulate a symmetrical LJ binary mixture > implementing LJ-PME methods. > > > The mixture is composed of A and B-type LJ particles and their sizes > (sigma) are

Re: [gmx-users] NMA eigenvectors doubts

Hi, I suspect the issue is related to the previous warning that you haven't minimized well enough. The diagonalization won't produce a full set of normal modes if the input coordinates are not at a stationary point. (Caveat, I've never used the method...) Mark On Wed, May 17, 2017 at 9:36 AM

Re: [gmx-users] NMA eigenvectors doubts

Maybe I figured the problem out!! The point is that my system is too big. I tried to minimize just the protein (6908 atoms) and the number of the matrix and the entries of the eigenvectors fit with the number of my system...I think Gromacs can not deal with system bigger than 15k atoms for the