Re: [gmx-users] multiple electric fields

As expected, multiple instances of a given component are not accepted by Gromacs. Is there anything that can be done? Can the functional form be extended to the current form + constant offset? The use scenario is very simple: photosensitive solid-state ion channels. It is that relatively rare

Re: [gmx-users] Calculation chi angle for tryptophan residue

http://manual.gromacs.org/documentation/2018.3/index.html Always check the manual. Highly recommend that everyone read / skim through every command when starting using GROMACS, gives you and overview of everything can do at that moment in time. And if wondering if can do something in

[gmx-users] multiple electric fields

Hi all, Is it possible to have an electric field of the form described here: http://manual.gromacs.org/documentation/2018.1/user-guide/mdp-options.html#mdp-electric-field-x%20;%20electric-field-y%20;%20electric-field-z but with a constant component? In other words, for a given component

[gmx-users] Best Force Field for Cellulose MD Simulations- Amending .dat & .rtp

Dear gmx-users, I'm quite new to GROMACS and I was wondering if anyone has advice for amending the residuetypes.dat file and the .rtp files within specific FF's for use in simulating Nanocellulose. The two FF's I'm currently trying to resolve errors on are: OPLSAA/M CHARMM36 My assumption

Re: [gmx-users] acpype

Check your python3, what's the command line for your python3? The shebang line (first line) in acpype.py is: #!/usr/bin/env python3 you need python3 to run acpype. If your default python is already python3, then change line to #!/usr/bin/env python python -V tells which python version you

Re: [gmx-users] acpype

Hi, Alan I have installed amber tools 18 for antechamber and acpype with git clone https://github.com/alanwilter/acpype.git then installed it with ln -s $PWD/acpype.py /usr/local/bin/acpype I didn't install open babel because my input files are in mol2 format. when i reun the command acpype

Re: [gmx-users] How to generate a new xtc file with a membrane protein complex properly oriented along a given axis?

Thank you very much Dallas, it worked. Stéphane -- Haven't tried it, but seems to me you generate a .tpr file with the protein orientated correctly within the box, then use trjconv -fit Catch ya, Dr. Dallas Warren Drug

[gmx-users] xpm2ps (2018.3) does print axis labels

Hello, I have a problem with gmx xpm2ps (v5.1.4 and 2018.2) with a xpm files generated with gmx_mpi densmap. For example If I use the following xpm (1) and m2p (2) files and the following command the x and y labels are not plotted in the eps figure. Same behavior problem occurs if I did not

[gmx-users] And Ryzen 8 core/16 thread use

Dear Users, Does anyone have concerns/comments ( other than heat output of the processor ) in using the relatively new AMD Ryzen 7 2700 with Gromacs 18.3 or v19 and gromacs' ability to make use of the 16 threads along with a gtx1080ti ? thanks Paul -- Gromacs Users mailing list * Please

[gmx-users] Calculation chi angle for tryptophan residue

Hi, How can I plot a graph of chi angle of tryptohan residue over time from my trajectory file? What is the suitable command? Thank you. Regards, Muhammad Harith bin Zulkifli Tel:013-9307882 E-mail: hzu...@gmail.com -- Gromacs Users mailing list * Please search the archive at

[gmx-users] No default Angle types

Hello, After running gmx grompp I get multiple errors like the following: ERROR 568 [file topol_Other_chain_D2.itp, line 499]: No default Angle types This line corresponds to the angle (using angletypes) HN1 NN1 HN1 This angle (and all the other that I get errors for) is specified

Re: [gmx-users] gmx kill computer?

BS”D Dear Michael, ThermalTake PSU’s are better than many out there, but they aren’t the best. Here is a link discussing how the theoretical wattage rating of a PSU may not actually translate into enough watts in reality, especially under sustained load.