[gmx-users] Secondary structure analysis graph rescale

Hi to whom it may concern, I would to ask something regarding gmx do_dssp analysis in Gromacs version 5.1.4. Is there any way that we can rescale the y-axis and x-axis (for major and minor ticks) of the dssp output graph in .xpm format ? and how ? your helps is highly appreciated. Thank you.

Re: [gmx-users] Exclusion - determine neighboring atoms by atom indices or by bond connections?

Hi, On Wed, 26 Jul 2017 22:53 lan hoa Trinh wrote: > Dear Gromacs community, > In the Gromacs manual, if nrexcl = 3, that means atoms i+1, i+2, i+3 are > excluded from non-bonded interactions with atom i. I don't know how Gromacs > determine the neighboring atoms, based

Re: [gmx-users] Regarding indexing to calculate hydrogen bond autocorrelation function

Hi, You use a tool like gmx select to select all those atoms. Have a look at its help and examples. Mark On Wed, 26 Jul 2017 20:00 Dilip H N wrote: > yes thn how can i index the groups (say i want to calculate hbond b/w NH of > glycine and O of water)... > with

Re: [gmx-users] Secondary structure analysis graph rescale

Hi, http://manual.gromacs.org/online/m2p.html use gmx xpm2ps with m2p file to generate eps files. -- Regards, Nikhil Maroli -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Non Standard Residue in Amber

Hi, I have a non standard residue, FAD, Flavin Adenine Dinucleotide. I need to standardize it for running a simulation using Amber force field. I tried ACPYPE but it is not working for this particular residue. I also read that Parmed can be used for the same purpose, but I could not find how to

[gmx-users] how could i question there?

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Re: [gmx-users] Non Standard Residue in Amber

Hi, Probably all those tools work fine, but perhaps you haven't used them well. Unfortunately we can't guess what errors you may have made without more information... Mark On Wed, 26 Jul 2017 13:08 Souvik Dey wrote: > Hi, > > I have a non standard residue, FAD, Flavin

Re: [gmx-users] how could i question there?

You already did. Just mail . Regards Imamul On Thu, 27 Jul 2017 at 9:12 pm, faru honey wrote: > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read

Re: [gmx-users] Fatal error: Topology include file "drg.itp" not found

Hi, You need to provide a lot more information if you hope to get help. See http://www.gromacs.org/Support for tips. Mark On Thu, 27 Jul 2017 13:34 faru honey wrote: > Kindly help me in solving the problem, I’m using tutorial > >

[gmx-users] Regarding entropy of a protein-ligand complex

Hi, I am extremely new to gromacs and I want to calculate the entropy of a protein-ligand system. I have ran energy minimization and equilibriation on the complex. I have looked into gmx anaeig but I can't figure out how to do use this command to get the entropy. Can someone help me with an

Re: [gmx-users] units of gmx wham output

Capital {S-1} is to make it ^{-1}. It is for superscript. And the \N returns the text to the default state. So it is basically the y-axis name for xmgrace tool. If you plot your .xvg file by using xmgrace you will see kj/mol on your Y-axis title. Overall your energy unit is kj/mol which is

[gmx-users] Performance values

Where is it documented how the mdrun performance metrics are calculated ? I’ve looked here http://manual.gromacs.org/documentation/2016/user-guide/mdrun-performance.html and here

[gmx-users] gmx_mpi mdrun with multidir and tabulated bond potentials

Hello everyone, I'm currently trying to run an equilibration for replica exchange md using tabulated bond potentials. I am receiving an error message when I use more than ~900 tables. However, I'm my simulation needs 1014 tables. Here is my input: "mpirun -np 40 gmx_mpi mdrun

[gmx-users] G_MMPBSA

Hi all, I am trying to install g_mmpbsa gromacs package( http://rashmikumari.github.io/g_mmpbsa/) but it's not working. Can anyone please guide me through the installation process of this package? -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] G_MMPBSA

Hi, You should start by reading and following the installation guide of this non-GROMACS tool. If you have questions, asking on its forum is probably best ;-) And please do provide some detail and what you did and where it went wrong. Mark On Thu, 27 Jul 2017 18:14 S M Bargeen Turzo

[gmx-users] Simulation Restart

hello, I am using this order to restart my simulation with gromacs 5.0 gmx_mpi mdrun -s npt.tpr -cpi npt.cpt however, the it dumps the results to traj.trr and md.log and not to the previous output files. anybody knows why? regards -- Gromacs Users mailing list * Please search the archive at

[gmx-users] error message: Invalid transform ...

Has anybody ever seen the following error message before? Program: gmx mdrun, version 2016.1 Source file: src/gromacs/fft/parallel_3dfft.cpp (line 173) *Fatal error:* *Invalid transform. Plan and execution don't match regarding reel/complex* -- Clinton King Graduate Student Chemistry

Re: [gmx-users] Simulation Restart

Hi, As the log file reports, it doesn't append because you chose output filenames (ie the default ones) that don't match what you originally chose. More recent versions of GROMACS refuse to run - you need to name all the output files the same way, or choose not to append. Mark On Thu, 27 Jul

Re: [gmx-users] Simulation Restart

If you want to use same name, and dump in the same file just add -deffnm previous_name -append To the existing command Yogesh > On 28-Jul-2017, at 12:56 AM, Mark Abraham wrote: > > Hi, > > As the log file reports, it doesn't append because you chose output >

[gmx-users] mdmat calculation of heavy atoms of two side chains

Dear gmx users, I would like to know about the hydrophobic interaction between heavy atoms of side chains in different chains of peptides. How can I use mdmat tool for this calculation? I separately indexed all heavy atoms but mdmat use only one index group in the calculation. I re-integrated

[gmx-users] gmx complains of mismatch between index and trajectory file

Hello, I'm using GROMACS 5.1.13 and ran into a problem I've never encountered before. I've run a simulation on a zinc-finger DNA complex and defined a group in my index filed called "Protein_DNA" from the default "Protein" and "DNA" groups. This group should contain 4666 atoms, which it does.

Re: [gmx-users] Simulation Restart

Hi, Only if that is what was done last time. The checkpoint knows exactly what was done, so do the same again! Mark On Thu, 27 Jul 2017 21:44 jay patil wrote: > If you want to use same name, and dump in the same file just add > -deffnm previous_name -append > To the