Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides

Hi Justin, I am asked to focus on learning how to change and update the CHARMM36 parameters, so I could implement the future changes and patches easier. (Thus, I am not focused in the Glycan Reader, at the moment.) Thank you! I think I now have a better understanding of what should I do. For e

[gmx-users] Regarding extending simulations with change in .mdp file

Hello, I have ran a energy minimization, followed by nvt, followed by md run. My md run mdp (ie., md.mdp) has dt = 0.002, nsteps = 3000 ; [0.002 * 3000 = 6 ps (60 ns)] nstxout = 5000 ; save coordinates every 10.0 ps nstvout = 5000 ; save velocities every 10.0 ps nstenergy = 5000 ; sav

Re: [gmx-users] PBC fix for visualization

I have found the cluster option of -pbc to work well for putting aggregates back together correctly. Some times you do need an index file and appropriate groups to assist with it getting it right. gmx trjconv -pbc cluster Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash

[gmx-users] Radial distribution function

Dear all, I have done a simulation for asphaltene in an organic solvent. The simulation produces a one cluster contains all the asphaltenes molecules in the system. I want to calculate the RDF and the cluster profile (i.e. maximum cluster, average cluster, etc.). Both of them shows strange results

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

Beg your pardon, I have not ignored your comment entirely regarding using specific residue COM. I just recently succeeded performing md_umbrella simulation (using protein COM) on few configurations. . I have not used specific residues COM so far as because of some confusions regrading defining it.

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

On 5/21/17 9:47 AM, abhisek Mondal wrote: I did try the code successfully on a configuration generated after pulling. The NVT approach with direction-periodic geometry worked nicely for the particular configuration. However, when I tried to reapply the same code (with modified COMs and thus pu

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

I did try the code successfully on a configuration generated after pulling. The NVT approach with direction-periodic geometry worked nicely for the particular configuration. However, when I tried to reapply the same code (with modified COMs and thus pull_vec) on a different configuration, somethin

Re: [gmx-users] Nonequilibrium simulations

I just reread my e-mail and realized that it was posed as a statement and not a question. What I meant was: When I run non-equilibrium simulations in the Gromacs code using "acc-groups", is the additional acceleration considered to contribute to the temperature when velocities are adjusted or not

Re: [gmx-users] Regarding extending simulations

and which are the commands tht i need to give there.. gmx trjconv or gmx grommp ..?? Can anybody guide me through this kindly.. Sent with Mailtrack On Sun, May 21,

[gmx-users] Regarding extending simulations

Hello, I have ran a energy minimization, followed by nvt, followed by md run. My md run mdp (ie., md.mdp) has dt = 0.002, nsteps = 3000 ; [0.002 * 3000 = 6 ps (60 ns)] nstxout = 5000 ; save coordinates every 10.0 ps nstvout = 5000 ; save velocities every 10.0 ps nstenergy = 5000 ; save

Re: [gmx-users] pdb2gmx do not work for unstable conformations

Dear Mark Abraham, Thank you so much for debugging it for me. The strange word could only be seen under Unix environment. After using dos2unix, the problem finally solves! I totally forgot to always use dos2unix. Thanks a lot for reminding me again! Yours sincerely Cheng -