[gmx-users] gmx rdf not reading gmx checked trr file.

Hi all. I'm having a problem with gmx rdf in some trajectories of mine. I'm dealing with several mixtures of two solvents in different concentrations. While I was dealing with the "non-infine dilutions", or when I had several molecules of each, gmx rdf calculated the rdfs with no error. Now,

Re: [gmx-users] Fatal Error when launching gromacs 2019.2 on GPU.

Hi, This is an issue in one of pre-detection checks that trips due to encountering exclusive / prohibited mode devices. You can work around this by entirely disabling the detection using the GMX_DISABLE_GPU_DETECTION environment variable. Cheers, -- Szilárd On Thu, Oct 17, 2019 at 5:01 PM

Re: [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

On 10/25/19 7:43 AM, Amit Jaiswal wrote: Dear Jorden, I tried the simulation by changing the residue number in .itp file but it still goes out of the box during NVT. As Justin mentioned that the naming of the residue is irrelevant, so I guess either I am doing some minor mistake in I had

Re: [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

Dear Jorden,I tried the simulation by changing the residue number in .itp file but it still goes out of the box during NVT. As Justin mentioned that the naming of the residue is irrelevant, so I guess either I am doing some minor mistake in topology naming. So, I have included the order of

Re: [gmx-users] how to select head groups of lipid within 10 angstrom of protein

On 10/25/19 5:38 AM, Peter Stern wrote: You are probably causing your command to run in the background with “&”. Try using “and” instead. In addition to this, the selection string needs to be enclosed by single quotes. -Justin Peter Sent from my iPhone On Oct 25, 2019, at 11:45 AM,

Re: [gmx-users] how to select head groups of lipid within 10 angstrom of protein

You are probably causing your command to run in the background with “&”. Try using “and” instead. Peter Sent from my iPhone > On Oct 25, 2019, at 11:45 AM, SHAHEE ISLAM wrote: > > Hi, > I am trying to calculate the angle between P and N vector of my lipid > (popc+popg) with regards to

[gmx-users] Obtaining stress-strain curves: Parrinello-Rahman, anisotropic and deform

Hi all, I’m pretty new to Gromacs and would like to obtain the stress-strain curves for a CH4/CO2 hydrate system where I apply the strain in one direction and obtain the corresponding stresses. Would someone be able to explain the use of the deform option and the corresponding pressure and

[gmx-users] how to select head groups of lipid within 10 angstrom of protein

Hi, I am trying to calculate the angle between P and N vector of my lipid (popc+popg) with regards to the z axis to see how the protein is affecting the membrane. I am using this command, but it does not working gmx select -f *.xtc -s *.tpr -select POPG & name P* N* within 1.0 of Protein -oi

Re: [gmx-users] QM/MM run tips or tutorials (Bogdanov, Vladimir)

Dear Vlad, Tutorials can be found at http://wwwuser.gwdg.de/~ggroenh/software.html Although the tutorials are outdated and were designed for much older version of GROMACS, most steps can still be run. Besides, the tutorials should help getting familiar with the QM/MM input. A newer tutorial,