Re: [gmx-users] How to compile Mopac7 with Gromacs_2016.3 release?

Good point! Thank you, Mark. Frank On 5/9/17, 5:20 PM, "Mark Abraham" wrote: >Hi, > >Such QM/MM support is effectively untested in GROMACS since the early days >of the implementation, so I would strongly

Re: [gmx-users] How to compile Mopac7 with Gromacs_2016.3 release?

Hi, Such QM/MM support is effectively untested in GROMACS since the early days of the implementation, so I would strongly suggest using the version of GROMACS that is either indicated in that install guide, or otherwise known to work e.g. by having been reported in a publication. Mark On Wed,

[gmx-users] How to compile Mopac7 with Gromacs_2016.3 release?

Hello, I am trying to get QMMM support in Gromacs. However, the instruction provided by Mopac 7 is using "./configure" with some parameters. However, starting from Gromacs 5, they use cmake to compile. Is that mean, if we want to use Mopac 7, we have to use the old version Gromacs, such as

Re: [gmx-users] How to use "gmx view" on Ubuntu?

Hi, Just like all normal installations of GROMACS, you need to run cmake from your build directory and tell it where the source directory is. The ".." works if the source is the parent directory, but if you're not following eg the installation guide, then you'll have to adapt! Mark On Tue, 9

Re: [gmx-users] How to use "gmx view" on Ubuntu?

Dear Gromacs and Mark Abraham, Sorry, I am not familiar with compiling issue. I installed xorg-dev by: sudo apt-get install xorg-dev Then, I type cmake .. -DGMX_X11=on But I was told: CMake Error: The source directory "/home/lanselibai/Cheng/gromacs/... ..." does not appear to contain

Re: [gmx-users] How to use "gmx view" on Ubuntu?

Hi, You'll need to install X11 headers and libraries (the package is called xorg-dev, off the top of my head), and use cmake .. -DGMX_X11=on before compiling & installing. Mark On Tue, May 9, 2017 at 8:59 PM ZHANG Cheng <272699...@qq.com> wrote: > Dear Gromacs, > I am running Gromacs 5.0.4 on

[gmx-users] How to use "gmx view" on Ubuntu?

Dear Gromacs, I am running Gromacs 5.0.4 on Ubuntu 14.04.1 LTS. When I run "gmx view ..." as below: gmx view -f dppc-md.xtc -s dppc-md.tpr I got the following: Compiled without X-Windows - can not run viewer. Can I ask how to use "gmx view" on Ubuntu? Thank you. Yours sincerely

[gmx-users] Fwd: Internal energy

Any comment please? Thanks. -- Forwarded message -- From: Alex Date: Tue, May 9, 2017 at 12:49 AM Subject: Internal energy To: gmx-us...@gromacs.org Hi gromacs user, A peptide(p), a solid surface(s) in water(w) solution are the three ingredients of

[gmx-users] B-FACTOR

The B-factor is indeed RMSF, precisely 8*pi**2*RMSF. At least formally. In practice it is the result of the refinement procedure that is used in crystallography. If you would like to calculate it, you should simulate a crystal. This is almost never done, but Bojan Zagrovich did it and compared

[gmx-users] Parameterizing Acetylated lysine: need for impropers?

Dear all, I am trying to adapt to Gromacs the parameters of acetylated lysine from 2 sources. First from http://ares.tamu.edu/FFPTM/ This webpage gives parameters in AMBER format. I've created a new residue in aminoacids.rtp coying the data from the Amber file. The Amber file contains the

Re: [gmx-users] B-FACTOR

Thanks for the answer ! I tired that too , but the problem is when we tired viewing the pdb structure in pymol and MOE software , both show different structural changes ... Can you please help me how to over come this problem. How to analyse the output file of B-FACTOR in pymol...? On 9 May

Re: [gmx-users] B-FACTOR

I am not sure but I think u can calculate t along with rmsf calculation where you have to generate additional output as pdb file. On Tue, 9 May 2017 at 6:58 PM, Kingsley Theras Primus Dass . < 105726...@gms.tcu.edu.tw> wrote: > Hi everyone ! > I want to calculate b-factor , but I don't kno how

[gmx-users] B-FACTOR

Hi everyone ! I want to calculate b-factor , but I don't kno how to calculate. Can anyone please tell me how to calculate b-factor for a protein and how to analyse it ... Thanks in advance -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Free energy calculations using tabulated potential

Dear GMX users, I am simulating metal ions in water by using user tabulated potentials to reproduce a customized force field pretty different from the standard 12-6-1. Is it possible to compute the free energy of hydration with BAR method by using potentials in this form? Thanks in advance

Re: [gmx-users] Error In Umbrella sampling.

Hi, It'd safe for general usage if your volume is already approximately correct. But it has been a frequent occurrence here that people follow tutorial methodology outside of that context, and use such coupling when that condition is not true, leading to failed simulations. We aim grompp warnings