[gmx-users] ERROR IN BASH SCRIPTING

Hi gromacs users, I use the following run.sh in the working directory of simulations #!/bin/bash set -e for ((i=0;i<27;i++)); do x=$(echo "0.05*$(($i+1))" | bc); sed 's/WINDOW/'$x'/g' mdp/min.mdp > grompp.mdp gmx grompp -o min.$i -pp min.$i -po min.$i -n index.ndx gmx mdrun

[gmx-users] Failed to execute command: Try specifying your dssp version with the -ver option.

Also, I have located dssp program in /usr/local/bin -- 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] Failed to execute command: Try specifying your dssp version with the -ver option.

Dear Gromacs users, I did MD simulation of my peptide on Gromacs 5.1.3. I want to do do_dssp analysis. After using following command: gmx_mpi do_dssp -f *.xtc -s *.tpr -n index.ndx -o -sc Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. According

Re: [gmx-users] Dihedral PCA documentation

Thank you Justin, that makes sense, thank you for help. However, I am struggling with the rest, due to lacking documentation & examples. Like Alex said, this web-page http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA is outdated, but there is no new version of it available... Or at

Re: [gmx-users] Dihedral PCA documentation

On 2/27/17 9:55 PM, Anna Vernon wrote: Thanks Justin, but I did use this command, which is supposed to be dihedral: g_angle -f h3_nowater.gro -n h3_ANGLE.ndx -or h3_ANGLE.trr -type dihedral Sure, but g_angle is only going to give you the options presented to it in the index file. If

Re: [gmx-users] Dihedral PCA documentation

Thanks Justin, but I did use this command, which is supposed to be dihedral: g_angle -f h3_nowater.gro -n h3_ANGLE.ndx -or h3_ANGLE.trr -type dihedral thanks A On 27/02/17 19:35, Justin Lemkul wrote: On 2/27/17 9:29 PM, Anna Vernon wrote: Thanks Alex. tried the new syntax, below the

Re: [gmx-users] Dihedral PCA documentation

On 2/27/17 9:29 PM, Anna Vernon wrote: Thanks Alex. tried the new syntax, below the output of g_angle, which did not get any easier... Хрень осталась...))) Group 0 (UB_th=108.4_297.062f) has36 elements Group 1 (UB_th=108.9_384.092f) has30 elements Group 2

Re: [gmx-users] Dihedral PCA documentation

Thanks Alex. tried the new syntax, below the output of g_angle, which did not get any easier... Хрень осталась...))) Group 0 (UB_th=108.4_297.062f) has36 elements Group 1 (UB_th=108.9_384.092f) has30 elements Group 2 (UB_th=109.7_794.962f) has 6 elements Group 3

Re: [gmx-users] Dihedral PCA documentation

I think you might be referring to the 2010 version of the online manual ( http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA), which is pretty outdated. A lot of syntax seems to be changing fairly rapidly, so хрень like this is to be expected. ;) The current manual points to gmx angle, gmx

[gmx-users] Dihedral PCA documentation

Dear Gromacs users, The documentation on Dihedral PCA analysis is confusing. Firstly, the links are redirecting to the main gromacs page which does not help because one needs to search for the specific commands from there. Secondly, -s option does not work in step 2: invalid command line

Re: [gmx-users] topology

On 2/27/17 12:49 AM, RAHUL SURESH wrote: I am explaining my issues regarding complex simulation. I have 200ns conformer(OPLS FF) I have generated my ligand gro and itp file.(Using topolgen1_1) I have edited my protein gro file and made it into complex file as per the tutorials. I have made

Re: [gmx-users] topology

On 2/27/17 12:21 AM, RAHUL SURESH wrote: There is a lot diference in topology generated using topolgen for OPLSAA and Gromos(Given in tutorial) For example, Topolgen gro file have mentioned forcefield type mentioned OPLSAA_140 for all atoms. Will that affect the simulation Do i need to make

Re: [gmx-users] topology

On 2/27/17 12:08 AM, RAHUL SURESH wrote: I have gone through the tutrial for protein ligand complex. I have managed to generatei tp and gro file for my ligand using topolgen. *Just insert a line that says #include "drg.itp" into topol.top after the position restraint file is included.*

Re: [gmx-users] How to define the sublayers in the simulation and update the list of molecules at t timeinterval

My first thought precisely. Have a sufficiently long "bulk" region above that nanotube and via pull code apply constant force to a layer of water at the top of that region, essentially creating a form of a piston. A more explicit version of this would be an actual piston subject to pulling. Also,

Re: [gmx-users] How to define the sublayers in the simulation and update the list of molecules at t timeinterval

Hi, You can't do any kind of dynamic updating of groups used for eg pulling. If you really need what you describe, then your only current option is to stop the simulation, run gmx select to generate new index groups and restart it. But I would consider alternatives, such as pushing (some of) the

Re: [gmx-users] Velocity as a function of distance Z

Hi, A group whose composition is defined geometrically over time requires constructing a dynamic selection, which is done with gmx select. Unfortunately that currently means writing a script to loop over frames, calling gmx select to make a suitable index file, then here e.g. gmx traj. Do check

Re: [gmx-users] topology

Le 27/02/2017 à 13:20, Dayhoff, Guy a écrit : I have made changes to my topol.top file. Now in my command for em.mdp I am getting 19 errors stating "NO DEFAULT BOND TYPE, ANGLE TYPE, ETC.” Dear Guy, Just to be sure, pay attention to the order of molecules in your top file, if your protein

Re: [gmx-users] PLUMED Meeting 2017

Dear users, Sorry for spamming your inbox. I have unintentionally sent this mail. Regards, Sudip On Mon, Feb 27, 2017 at 9:33 PM, Sudip Das wrote: > Dear Tarakda, > > As CCEM meeting is from 15th to 20th May, should I attend this PLUMED > meeting also (22-27th May)?

Re: [gmx-users] PLUMED Meeting 2017

Dear Tarakda, As CCEM meeting is from 15th to 20th May, should I attend this PLUMED meeting also (22-27th May)? What do you suggest? Yet I haven't talk to sir regarding this. Regards, Sudip On Mon, Feb 27, 2017 at 9:11 PM, Giovanni Bussi wrote: > Dear all, > > this meeting

[gmx-users] PLUMED Meeting 2017

Dear all, this meeting might be relevant for gromacs users, so we also post it here. Atomistic simulations play a fundamental and ever-increasing role in biophysics, molecular biology, chemistry, and condensed-matter physics. Unfortunately, the large numbers of particles in realistic systems and

[gmx-users] rdf calculation with respect to center of mass

Dear gmx-users, The radial distribution function with respect to center-of-mass was computable in old gromacs versions. How can I calculate that  in newer version(2016)? Thanks in advance. Maryam -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] TOPOLBUILD 1.3

> Date: Mon, 27 Feb 2017 07:26:23 + > From: "Subashini .K" > To: "gmx-us...@gromacs.org" > Subject: [gmx-users] TOPOLBUILD 1.3 > Message-ID: > > > >

Re: [gmx-users] How to define the sublayers in the simulation and update the list of molecules at t timeinterval

Dear GROMACS users, I am working on 'Desalination process with CNT based membranes', where I want to apply pressure gradient across CNT channel. I have fixed CNT channel in z direction. This CNT channel is connected with NaCl solution reservoir at top and fresh water reservoir at bottom. Now I

Re: [gmx-users] topology

On Feb 27, 2017, at 6:00 AM, gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: I am explaining my issues regarding complex simulation. I have 200ns conformer(OPLS FF) I have generated my ligand gro and itp file.(Using

[gmx-users] Velocity as a function of distance Z

Dear gmx-users, I have several simulations regarding atoms flowing between two gold surfaces. The flow of the liquid molecules show a distinct Poiseuille flow, which was expected. I am now interested in extracting the velocities of these liquid molecules (total of around 3 atoms, around 700

Re: [gmx-users] Protein and Ligand position restraint

Thank you Justin, Got it Amir On Sun, Feb 26, 2017 at 7:52 AM, Justin Lemkul wrote: > > > On 2/24/17 1:19 AM, Amir Zeb wrote: > >> Hello gmx users, >> >> I want to conduct md simulation to explore the comparative stability and >> interaction mechanism of the reference compound