[gmx-users] Fw: Attempting REMD tutorial by Mark Abraham

From: Israel Estrada Sent: Wednesday, May 29, 2019 3:15 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Attempting REMD tutorial by Mark Abraham Hi all, I'm attempting to follow Mark Abraham's introduction to REMD.

Re: [gmx-users] Segmentation fault, core dumped error

https://redmine.gromacs.org/account/register Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you

Re: [gmx-users] Segmentation fault, core dumped error

Hi Paul Bauer, I do not have an account on redmine.gromacs.org neither that page allows me to create an account. Please let me know what to do. Hi Najamuddin, I tried xtc file instead of trr, still same error shows up. Thank you, Neena From: Neena Susan

[gmx-users] proper use of restraints

Dear Users, I’ve modeled a simple polymer ( nylon ), 600 atoms aligned in the x direction . I create a restraint file for one molecule using the top file indices and fx,fy fz = 1 0 0 then place 10 to 100 copies in a box On equilibration, they exhibit the expected hydrogen bonding

Re: [gmx-users] Segmentation fault, core dumped error

Instead of .trr file you can use .tpr and .xtc file On Wed, May 29, 2019, 10:25 PM Neena Susan Eappen < neena.susaneap...@mail.utoronto.ca> wrote: > Command: gmx hbond -f md_0_1.trr -s md_0_1.tpr > > Specify 2 groups to analyze: > > Group 0 (System) has 130 elements > > Group 1

Re: [gmx-users] Gromacs error

http://manual.gromacs.org/documentation/current/onlinehelp/gmx-covar.html Has the following note (as does 'gmx help covar'): "Note that the diagonalization of a matrix requires memory and time that will increase at least as fast as than the square of the number of atoms involved. It is easy to run

[gmx-users] Calculation of free energy of distance restraints alone

Hello Everybody, I am trying to determine the free energy of restraining and "un-restraining" a protein-RNA complex while leaving on vdw and coulomb interactions. My current free energy parameters are the following for one of the mdp files in the lambda_state; ; Free energy control stuff

Re: [gmx-users] Segmentation fault, core dumped error

Command: gmx hbond -f md_0_1.trr -s md_0_1.tpr Specify 2 groups to analyze: Group 0 (System) has 130 elements Group 1 (Protein) has 130 elements Group 2 (Protein-H) has63 elements Group 3 (C-alpha) has11 elements Group 4 (Backbone) has34 elements Group

Re: [gmx-users] Stress-Strain curve plot

Hi, Thank you very much for your answers. There are many questions that I have searched online and looked up in GROMACS manual but still confused, so I asked here. Your answers help to clarify them a lot for me. I really appreciate it. However, there are some questions that I'm still not very

Re: [gmx-users] Explaination of some terminology

On 5/29/19 4:07 AM, Anh Vo wrote: Hi all, I'm new to GROMACS and there are some terms that I’m not very clear when reading GROMACS materials. I have looked them up and read more but I’m still confused. Please help me to clarify them. - What is improper vs. proper dihedral? -

[gmx-users] Gromacs error

Dear GROMACS Developers and users, While trying to clustering analysis based on certain distance matrices, however, while trying to perform PCA, I executed the following command, it shows the following error. Need your valuable suggestion and feedback to get rid of such errors. Thanking you

[gmx-users] Question of constraining bonds

Dear all gromacs users,I'm new to gromacs, and I have some questions about bond constraints.Now I have a system with methane, hydrogen, and TIP4P/Ew water. In special, topology of hydrogen molecule is including [ constraints ], for constructing a virtual site in the center of hydrogen

Re: [gmx-users] Segmentation fault, core dumped error

Hello, can you please open a new issue on redmine.gromacs.org for this, and upload your input files (if possible) and the command line you used that caused the error? Thanks Paul On 29/05/2019 01:31, Neena Susan Eappen wrote: Hello gromacs users, Is there a reason why segmentation fault

[gmx-users] GROMACS 2018.7 patch release available

Hi GROMACS users, I just released another patch release of GROMACS 2018, bringing the official version to 2018.7! We decided to release this additional patch due to issues found in 2018.6 that could affect scientific correctness, so we encourage all users of the 2018 series to update to

Re: [gmx-users] Timestep in GROMACS simulation

Hi, > I'm still not clear what "sampling" means. Does it mean collecting data > from the simulation? Pretty much. The point of a molecular dynamics simulation is to calculate structural, thermodynamic, etc... properties of some system from the microscopic dynamics of atoms/molecules/whatever.

Re: [gmx-users] Computational electrophysiology (compEL) setup issues (Kutzner, Carsten)

Dear Francesco, > On 29. May 2019, at 10:01, Francesco Petrizzelli > wrote: > >> A cyl0-r (and cyl1-r) of 0.7 nm is too small for a pore radius of 3 A to >> reliably track the ions, some might sneak through your channel without being >> recorded in the cylinder. Rather choose this value a

Re: [gmx-users] Computational electrophysiology (compEL) setup issues (Kutzner, Carsten)

Thank Dr Kursten for your reply. I really apprecciate your work on compEL. >It is even easier to just generate a single bilayer with a channel, and then >duplicate the whole system by stacking two copies on top of each other, e.g. >with the script found on page