Hila Failayev

4 Questions 1 Answers 0 Followers

Questions related from Hila Failayev

Is GROMACS minimization maximum force reasonalble?

Hi, An energy minimization step I converged to machine precision with the following values: Potential Energy = -5.0373220e+06 Maximum force = 1.1988365e+03 on atom 6641 Norm of force =...

09 April 2023 3,070 2 View

How to make a disulfide bond between two seperate chains using GROMACS 5.1.4?

Hello everyone, I' trying to simulate a system with multiple chains. According to the PDB entry, there is a single disulfide bond connecting two of the chains. Unfortunately, 'pdb2gmx' with '-ss'...

19 June 2019 6,820 2 View

How to simulate methylated Arginine in MD?

Hello, I've modeled two structures of peptides, each with a different type of methylation on an Arg residue: N-methylation (on the C-alpha) and a methylation on one of the NH2 groups of it's R...

20 September 2018 9,654 0 View

Is targeted MD available in GROMACS?

up from version 4.6.7 and above.

22 December 2015 7,904 1 View