[gmx-users] gmx dos - Possible bug on 5.0.6

Hi all! I've been running gmx dos (version 5.0.4) in some trajectories with the following: echo BEN | gmx_504 dos -s ben.DOS.tpr -f ben.DOS.trr -g ben.log -dos dos.xvg -vacf vacf.xvg -mvacf mvacf.xvg and it runs just fine. But when I run the same line with 5.0.6, I get:

Re: [gmx-users] chemical potential differences between two component liquids and crystal structures in gromacs

Chemical potential in the fluid would be almost exactly the sanme to a solvation calculation -- as long as you can count on it to be metastable enough to not crystalize / phase separate during the time of the simulation. Chemical potential in the crystal is . . . harder. Check out the

[gmx-users] chemical potential differences between two component liquids and crystal structures in gromacs

Hello everyone, I am interested in calculating the change in chemical potential between a metastable liquid, consisting or solvent and solute, and the crystal structure of the pure solute. For instance, one system I am looking at is tetrolic acid in CCL4 as my metastable liquid, and one of

[gmx-users] Calculating RDF Using Closet Atom

Dear GMX Users, Sorry to take your valuable time. I have a mixed liquid system simulated using gromacs version 5.0.4, where I want to calculate radial distribution between molecule type A and type B defining the distance between them by either center of mass of Molecule A - closet atom to

[gmx-users] probability distributions in gmx

Dear gmx, I understand that probability distributions of distance can be calculated through gmx analyze tool but how the probability distributions of others such as SASA and secondary structure can be calculated? Do i have to use other plotting tool R, gnuplot to do ? or can any gromacs

[gmx-users] Helicity over simulation time?

Dear all, I have performed 200ns simulation for a protein and wants to plot a helicity over simulation time. After reading few queries, i have done do_dssp and obtained the scount.xvg which has the all secondary structure as a function time. I wonder, how do i only obtain the helicity over

Re: [gmx-users] Heat autocorrelation function

Is it possible to write heat current vector j in trr file ( by using suitable mdp file) so that we may extract it to find heat current autocorrelation ? On 25 Aug 2015 12:43, David van der Spoel sp...@xray.bmc.uu.se wrote: On 25/08/15 05:14, Sunil Ghimire wrote: I want to use green- kubo

Re: [gmx-users] g_sham

It's working now. Thanks a lot. One more query: If I am interested in getting frames near the minimia and not actually on it, how do I change the last if-statement? On Mon, Aug 24, 2015 at 5:45 PM, Smith, Micholas D. smit...@ornl.gov wrote: My bad, I had a typo, try this one: awk -v

Re: [gmx-users] Single point energy calculations

Hi, On Tue, Aug 25, 2015 at 6:30 AM soumadwip ghosh soumadwipgh...@gmail.com wrote: Hello all, I am trying to calculate the single point energies of my system (a nucleic acid and a nanoparticle) to ultimately estimate the E(interaction). I am following this paper.

[gmx-users] No ./configure file

I was trying to download grimaces. But it says, No such file or directory I tried make, but that too gave an error. It said, No targets specified and no make file found. I tried installing version 5.1, 5.0 and 4.6. However, the same error persists. Please help! -- Regards, Raag -- Gromacs Users

Re: [gmx-users] Heat autocorrelation function

On 25/08/15 05:14, Sunil Ghimire wrote: I want to use green- kubo formalism , which uses the integral of autocorelation of heat flux J to calculate thermal conductivity. You may also want to check other gromacs tools like g_current and another one of which I forgot the name. On 24 Aug 2015

Re: [gmx-users] Randomly alter pdb start coordinates

Hi, On Tue, Aug 25, 2015 at 5:08 AM PER HENRY ANDREAS WITTLER 17526...@students.latrobe.edu.au wrote: There is mentioned that for re-running an MD run for better statistics, it can be good to change starting coordinates, besides the seed, is there a gmx command which is used for randomly

[gmx-users] Comparing various MD packages

Hello all, I am interested in comparing various MD packages like LAMMPS, GROMACS, DESMOND, NWChem, RedMD. I was looking through literature to find any relevant papers regarding the same and found a paper or two that do so. But they used different set of bench-marking problem sets, and no single

Re: [gmx-users] How do I calculate the difference between two energy values?

I believe that this is a statistics question and not a gromacs question :-). 51.4 +/- 1.33 kJ/mol Sent from my iPad On 25 באוג׳ 2015, at 14:44, minky son minky0...@gmail.com wrote: Dear GROMACS users, I have been studying free energy calculation in Justin tutorial. I performed VDW

[gmx-users] Dihedral Angle Cross-correlation Function

Hi All, I was wondering if there is a way to calculate the cross-correlation function between a pair of dihedral angles. I see GROMACS does have programs for dihedral angle autocorrelation function estimation (g_chi, g_angle), but that deals with correlation of a specific dihedral angle with

[gmx-users] Input files for performance analysis

Hello all, I have good enough experience in high performance and parallel computing and would like to find out bottlenecks in various phases of GROMACS. Can anyone please give me links to ready-to run input files of standard molecular systems to be simulated for GROMACS (to be run on

[gmx-users] Bond rotation freedom or mobility

Hello GROMACS users, I am interested in quantifying the freedom or mobility of specific carbon-carbon single bonds in a organic molecule. Does anyone know the most appropriate method to do this? Can I make use of gmx chi? Best, Eric -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] mdrun writes gro file in two different formats and failed visualization of trajectories

Hi, Quick nitpick... Justin's right on the important points, but note that mdrun -nt may (or may not) use domain decomposition depending on the .tpr settings and the way GROMACS was configured. (e.g. a build with OpenMP and thread-MPI is permitted to use either, and the latter triggers the use of

[gmx-users] em.gro file doesnt show a reasonable structure in VMD

Dear gmx users, I have perform an energy minimization on my system and the potential per step plot has a normal appearance, but the em.gro file doesn't show a reasonable structure in VMD. Could you tell me why this happened? Regards, Farideh -- Gromacs Users mailing list * Please search the

[gmx-users] Testing gromacs on IBM POWER8

Hello there We've been testing gromacs-5.1-beta1 in an IBM POWER8. The input used is 'pme.mdp' within the .96 directory of the following benchmark: ftp://ftp.gromacs.org/pub/benchmarks/water_GMX50_bare.tar.gz The following link shows our results:

Re: [gmx-users] gmx dos - Possible bug on 5.0.6

On 25/08/15 18:24, Marcelo Depólo wrote: Hi all! I've been running gmx dos (version 5.0.4) in some trajectories with the following: echo BEN | gmx_504 dos -s ben.DOS.tpr -f ben.DOS.trr -g ben.log -dos dos.xvg -vacf vacf.xvg -mvacf mvacf.xvg and it runs just fine. But when I run the same line

[gmx-users] Gromacs-5.1 XLC Seg. Fault.

Hello guys. I've compiled Gromacs-5.1 with XLC 13.1.2 + ESSL and FFTW (altivec enabled) but I'm getting seg. fault while trying to run it. I'm testing it with .96 workload. Here's its input: http://pastebin.com/Ezp95b2B Here's the error I'm getting: [ubuntu:19418] *** Process received

Re: [gmx-users] Single point energy calculations

Thanks Mark. I will do it..:-) Regards, Soumadwip -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit

[gmx-users] How do I calculate the difference between two energy values?

Dear GROMACS users, I have been studying free energy calculation in Justin tutorial. I performed VDW decoupling and coulomb decoupling simulations separately. I obtained the free energy values for each simulation using gmx bar. coulomb decoupling simulation = 60.88 +/- 0.23 kJ/mol VDW

Re: [gmx-users] em.gro file doesnt show a reasonable structure in VMD

Hi, Thanks for the answer. I have shred the files via dropbox: https://www.dropbox.com/sh/bgcnpwrbvj7ocxg/AAAFKNlpEs5BREDmFPWoUfGma?dl=0 Truly yours, Farideh On Tue, Aug 25, 2015 at 3:21 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Not with that little information. Is the starting

Re: [gmx-users] em.gro file doesnt show a reasonable structure in VMD

Hi, Not with that little information. Is the starting structure reasonable? Upload a screenshot to a file sharing service and show us what you think is unreasonable :-) Mark On Tue, Aug 25, 2015 at 12:16 PM faride badalkhani farideh.kham...@gmail.com wrote: Dear gmx users, I have perform

Re: [gmx-users] No ./configure file

Hi, We've been using cmake as the only build system for GROMACS for 2.5 years now. :-) Please read more in the install guide! Mark On Tue, Aug 25, 2015 at 11:00 AM Raag Saluja saluja.r...@gmail.com wrote: I was trying to download grimaces. But it says, No such file or directory I tried make,

Re: [gmx-users] gmx dos - Possible bug on 5.0.6

2015-08-25 17:29 GMT-03:00 David van der Spoel sp...@xray.bmc.uu.se: On 25/08/15 18:24, Marcelo Depólo wrote: Hi all! I've been running gmx dos (version 5.0.4) in some trajectories with the following: echo BEN | gmx_504 dos -s ben.DOS.tpr -f ben.DOS.trr -g ben.log -dos dos.xvg -vacf

Re: [gmx-users] gmx dos - Possible bug on 5.0.6

On 8/25/15 5:03 PM, Marcelo Depólo wrote: 2015-08-25 17:29 GMT-03:00 David van der Spoel sp...@xray.bmc.uu.se: On 25/08/15 18:24, Marcelo Depólo wrote: Hi all! I've been running gmx dos (version 5.0.4) in some trajectories with the following: echo BEN | gmx_504 dos -s ben.DOS.tpr -f

Re: [gmx-users] Bond rotation freedom or mobility

On 8/25/15 2:31 PM, Eric Smoll wrote: Hello GROMACS users, I am interested in quantifying the freedom or mobility of specific carbon-carbon single bonds in a organic molecule. Does anyone know the most appropriate method to do this? Can I make use of gmx chi? No, gmx chi is specific for

Re: [gmx-users] em.gro file doesnt show a reasonable structure in VMD

On 8/25/15 7:51 AM, faride badalkhani wrote: Hi, Thanks for the answer. I have shred the files via dropbox: https://www.dropbox.com/sh/bgcnpwrbvj7ocxg/AAAFKNlpEs5BREDmFPWoUfGma?dl=0 You have no bonded interactions defined in your topology, so naturally everything flies apart. -Justin

Re: [gmx-users] Membrane protein insertion

Thanks! My protein is 200 amino acids single chain molecule. I tried the minimization in vacuo (potential.xvg), using the em.mdp file (see attached). I feel that the system is not really minimized. I check the pdb file and it seems ok. Shall I start again with the in vacuum minimized