Re: [gmx-users] g_dist equivalent in Version 5.*

Thanks a lot. This does indeed help) Sincerely Max. > On Jan 25, 2019, at 22:09, Mark Abraham wrote: > > Hi, > > Does > http://manual.gromacs.org/documentation/current/user-guide/cmdline.html#command-changes-between-versions > help? > > Mark > >> On Fri., 25 Jan. 2019, 10:29 Max

Re: [gmx-users] Change PBC box size after simulation.

Thank you for your response. Yes my input to `trjconv -s` has my system in such way that I can make all my desired calculations (as far as I can see in VMD). Sincerely Max. > On Jan 25, 2019, at 22:11, Mark Abraham wrote: > > Hi, > > What property do you want to make true? Does your

Re: [gmx-users] Calculating tilt angle with respect to the membrane normal

Finally, I visualized the data in the output file of -otilt (tilt_TMC1CA.xvg) using xmgrace with the command: xmgrace -nxy tilt_TMC1CA.xvg I read again the documentation of gmx helixorient and if I understood well, the values of the tilt angle of the helix axis to the membrane plan are

Re: [gmx-users] Nonsense timing accounting with OpenCL in Haswell

Hi, Roland, Thank you for your response. If the GT2 GPU won't give much acceleration, I'm not sure that it's worth to fix the timing issue in beignet, since it's deprecated. Not much sense in trying to make a deprecated driver work so an ineffective GPU can be used. I'll be testing a GTX 1050Ti

Re: [gmx-users] "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters

Dear All, (hope this message can be put under the original thread) I solved this problem. The reason is, I was trying to fill the system with water then minimise it, which is not good. The better way is, prepare a waterbox that is even larger than the system box. Then minimise that water

Re: [gmx-users] g_dist equivalent in Version 5.*

Hi, Does http://manual.gromacs.org/documentation/current/user-guide/cmdline.html#command-changes-between-versions help? Mark On Fri., 25 Jan. 2019, 10:29 Max Adamyan, wrote: > Hi. I know you can compute distances of mass center's of two atom groups > using `g_dist` command. But I cannot find

Re: [gmx-users] (no subject)

Hi, This is one of the examples in the documentation of gmx select. Try looking there! Mark On Fri., 25 Jan. 2019, 07:30 Soham Sarkar, wrote: > Hello Everyone, >I want to calculate some properties of the solvent molecules within > 6angstrom from the protein backbone, for that I need a

Re: [gmx-users] pdb2gmx error due to terminal capping of peptide

Hi, Leave the rtp the way it was and name the residue in the pdb file so that it matches. Then you won't have to teach pdb2gmx that your newly invented residue is protein Mark On Fri., 25 Jan. 2019, 05:51 Neena Susan Eappen, < neena.susaneap...@mail.utoronto.ca> wrote: > Hi GMX users, > > >

Re: [gmx-users] how to generate the topology files for beta-cyclodextrin using gmx?

pdb2gmx isn't acceptable for any molecule. Only for proteins and DNA-RNA. β-cyclodextrin is present in atb.uq.edu.au in many variants for force field G54A7FF Or it is quit simple to build β-CD with glycan builder and modeller from charrm-gui.org (7 times connect α glucose with 1-4 link). One

[gmx-users] ion population in between my systems

Hi everyone, I am trying to calculate the number of ions that passes through my system with respect to time. I have Sodium ions as well as Calcium ions. I would like to calculate for these ions individually. I tried using gmx rdf but it seems the command I am using is wrong. How do I specify

[gmx-users] Calculating tilt angle with respect to the membrane normal

Dear GMX users, I would like to calculate the angle of a transmembrane helix long axis with respect to the membrane normal and see how this angle fluctuates during the simulation. In the forums, people were suggesting to use gmx helixorient. I used it with the following command: gmx

[gmx-users] Change PBC box size after simulation.

Hi. After simulation, I have trajectory file with broken and jumping atoms. I've fixed broken atoms, and some of jumping, but no-meter how hard I try, I cannot get rid of all of it. I've read Gromacs suggested workflow

[gmx-users] g_dist equivalent in Version 5.*

Hi. I know you can compute distances of mass center's of two atom groups using `g_dist` command. But I cannot find command that does the same in Gromacs version 5.* I know `gmx distance`, but it calculates pairwise distances in one selection. And `gmx pairdist` which calculates only min or max