Re: [gmx-users] CMAP format on GROMACS

On 1/8/20 10:25 AM, Marcelo Depólo wrote: Thanks for your input, Justin. Helpful as always. I am assuming the array is formatted to vary phi as a function of psi i.e. (-180,-180), (-180,-165), (-180,-150) [considering (phi,psi)] and again but for phi = -165. I am also assuming that, since

Re: [gmx-users] Comparing the RMSD of an in silico variant to a crystal structure.

On 1/8/20 11:12 AM, Matthew Fisher wrote: Dear all, I'm simulating the effect of amino acid mutations on tertiary structure and, for benchmarking purposes, I want to compare the RMS of my in silico variant trajectories (prepared from the WT structure) to their cystallographic structures.

Re: [gmx-users] Vibrational spectra of amide I using gromacs

Dear Mijiddorj, It is a matter of taste, but I like to use xmgrace for that kind of analysis. The GROMACS tool gmx analyze can do that for you: http://manual.gromacs.org/documentation/5.1/onlinehelp/gmx-analyze.html Andre On Wed, Jan 8, 2020 at 9:18 PM Mijiddorj B wrote: > Dear Andre > >

Re: [gmx-users] Vibrational spectra of amide I using gromacs

Dear Andre Thank you very much for your quick response. I am very new for this type of analysis, and I would like to ask further. I am sorry for that. Is there any good software? If you have any experience, please suggest me some useful software for the time series correlation and the Fourier

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 189, Issue 18

Dear Andre Thank you very much for your quick response. I am very new for this type of analysis, and I would like to ask further. I am sorry for that. Is there any good software? If you have any experience, please suggest me some useful software for the time series correlation and the Fourier

Re: [gmx-users] Comparing the RMSD of an in silico variant to a crystal structure.

Use the .tpr file generated by grompp module On Wed 8 Jan, 2020, 9:43 PM Matthew Fisher, wrote: > Dear all, > > I'm simulating the effect of amino acid mutations on tertiary structure > and, for benchmarking purposes, I want to compare the RMS of my in silico > variant trajectories (prepared

[gmx-users] Comparing the RMSD of an in silico variant to a crystal structure.

Dear all, I'm simulating the effect of amino acid mutations on tertiary structure and, for benchmarking purposes, I want to compare the RMS of my in silico variant trajectories (prepared from the WT structure) to their cystallographic structures. In the gmx rms command, when I select the

[gmx-users] is GPU peer access(RDMA) supported with inter-node and gmx2020 mpi version?

Hi, is GPU peer access(RDMA) supported with inter-node and gmx2020 mpi version on NVidia GPU? or just work only in single-node with threadMPI via Nvidia GPU direct? Thanks, Jimmy -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] cant compute msd

After removing the -mol command it worked fine. On Wed, Jan 8, 2020, 3:53 PM Christian Blau wrote: > Hi Devargya, > > > I believe it's the mixture of -mol and -o options at the same time that > leads to the unexpected behaviour - there can > only be one .xvg output for this tool and we'll see

Re: [gmx-users] CMAP format on GROMACS

Thanks for your input, Justin. Helpful as always. I am assuming the array is formatted to vary phi as a function of psi i.e. (-180,-180), (-180,-165), (-180,-150) [considering (phi,psi)] and again but for phi = -165. I am also assuming that, since it is a 24x24 matrix, values will start in

Re: [gmx-users] Vibrational spectra of amide I using gromacs

Should be doable using any standard spreadsheet: (1) save the bond lengths along the simulation for the bond of interest (2) compute the time correlation function for these bond lengths (the autocorrelation function for this time series) (3) compute the Fourier transform of the time correlation

Re: [gmx-users] Position restrains calculation of virial

Hi Johannes, On Wed, Jan 8, 2020 at 11:29 AM Johannes Hermann wrote: > Dear all, > > how is the virial computed when position restraints are applied? Are > forces due to position restrains included or excluded? > > Yes the the forces due to position restrains are included. But I think that

[gmx-users] Vibrational spectra of amide I using gromacs

Dear gmx users, Hello, I would like to ask vibrational spectra of amide of specific amino acids. Is it possible to analyze from classic MD calculations of gromacs? Or Is there any software that is compatible with gmx trajectories to calculate the spectra? Best regards, Mijiddorj -- Gromacs

Re: [gmx-users] system has non zero net charge

On 1/8/20 6:01 AM, Yogesh Sharma wrote: Greetings, I am performing membrane protein simulation in the presence of a biomolecule. topology for the molecule was downloaded from ATB server. After simulation run, I found unexpected behviour of the added biomolecule. This ligand named UINL was

Re: [gmx-users] Index group for Backbone/C-alpha of specific stretch of residues

On 1/8/20 4:49 AM, Christian Blau wrote: Hi Navnett, gmx select will be your friend. At the bottom of http://manual.gromacs.org/documentation/current/onlinehelp/selections.html you'll find some example commands. Something along the lines of   gmx select -select 'name CA and resid >

Re: [gmx-users] Simulated Annealing command line

On 1/7/20 6:35 PM, Neena Susan Eappen wrote: Hi Justin, Thank you for your answer. I haven't written scripts before, so I was wondering is there a sample script I can see for looping in gromacs. What you're trying to do is similar to the logic in

[gmx-users] how to set system for absolute free enegy calculation of ligand in protein

Dear Gromacs users I need your suggestions regarding the calculation of free energy of binding in of ligand protein-ligand complex in setting up the system. I am performing binding free energy calculation following alchemical free energy path. I added a single molecule type in topology for both

Re: [gmx-users] system has non zero net charge

Hi Yogesh, this happens to me as well sometimes, there are several options: - your protein is not neutral (my best practice is to you use pdb2gmx interactively and set the charges for all amino acids manually following pkA predictions by e.g. Propka - then you will immediately know if the

[gmx-users] system has non zero net charge

Greetings, I am performing membrane protein simulation in the presence of a biomolecule. topology for the molecule was downloaded from ATB server. After simulation run, I found unexpected behviour of the added biomolecule. This ligand named UINL was showing affinity to ASP and GLU residues.

[gmx-users] Position restrains calculation of virial

Dear all, how is the virial computed when position restraints are applied? Are forces due to position restrains included or excluded? Thanks! All the best Johannes -- __ *Technische Universität München* *Johannes Hermann, M.Sc.* Lehrstuhl für

Re: [gmx-users] cant compute msd

Hi Devargya, I believe it's the mixture of -mol and -o options at the same time that leads to the unexpected behaviour - there can only be one .xvg output for this tool and we'll see to having it fixed. Do you get any diff_mol.xvg files instead? The documentation states that "If -mol is

[gmx-users] cant compute msd

hi, when i am using the command gmx msd -f prd.xtc -n il.ndx -s out3.tpr -mol -o msd.xvg after that choosing a group the following line is coming. Select a group to calculate mean squared displacement for: Group 0 ( System) has 5616 elements Group 1 ( Other) has 5616

Re: [gmx-users] How to rotate the molecule in box

Hi Yeping, The center of rotation is (0,0,0) for the rotate command, which is the lower left front corner of your box, and not the box center. That's why the molecule moves out of the box when rotating. One (of conceivable more ways) to perform the rotation, is to use -center (0,0,0) to

Re: [gmx-users] Index group for Backbone/C-alpha of specific stretch of residues

Thank You, Sir! On Wed, Jan 8, 2020 at 3:19 PM Christian Blau wrote: > Hi Navnett, > > > gmx select will be your friend. > > > At the bottom of > > http://manual.gromacs.org/documentation/current/onlinehelp/selections.html > > you'll find some example commands. Something along the lines of > >

Re: [gmx-users] Index group for Backbone/C-alpha of specific stretch of residues

Hi Navnett, gmx select will be your friend. At the bottom of http://manual.gromacs.org/documentation/current/onlinehelp/selections.html you'll find some example commands. Something along the lines of   gmx select -select 'name CA and resid > 149 and resid < 211' should work. It's a very

Re: [gmx-users] Index group for Backbone/C-alpha of specific stretch of residues

Sorry, it should be 150-200 residues. On Wed, Jan 8, 2020 at 3:09 PM Navneet Kumar wrote: > Hello Everyone! > > > How to create an index group for Backbone/C-alpha for a specific set of > residues from protein? (Say Protein with 200 amino acid; want to create an > index group for the backbone

[gmx-users] Index group for Backbone/C-alpha of specific stretch of residues

Hello Everyone! How to create an index group for Backbone/C-alpha for a specific set of residues from protein? (Say Protein with 200 amino acid; want to create an index group for the backbone of residues 150-210). Regards Navneet Kumar -- Gromacs Users mailing list * Please search the archive

Re: [gmx-users] Make index command in gromacs

Hi Shan, gmx select gives you many more options to do complex arithmetic with selections that might help you here. You can try using gmx select -select "SELECTION STING" you'll find lots of selection string examples at the bottom in here:

Re: [gmx-users] Make index command in gromacs

Hi, Maybe you could use gmx select to generate your index file http://manual.gromacs.org/documentation/current/onlinehelp/gmx-select.html?highlight=select Best regards Alessandra On Tue, Jan 7, 2020 at 11:39 PM Shan Jayasinghe < shanjayasinghe2...@gmail.com> wrote: > Dear Gromacs Users, > >