Re: [gmx-users] Buggy 2020?

Hi, Based on what is in your system, what do you think the behavior should be? A change reflects that one of the versions may be wrong, but not that the new one is necessarily it. Mark On Fri, 10 Apr 2020 at 08:17, Parvez Mh wrote: > Hello All, > > I am wondering if gromacs-2020 is buggy? or

Re: [gmx-users] Regarding version of gromacs

On 4/10/20 9:20 PM, Ashma Khan wrote: Thank you Justin for your suggestion As I run my simulation on supercomputer and there is availability of gromacs-5.1.2 version not 5.1.4. Earlier it had 5.1.4 version but now it has only 5.1.2 version. You can always install the version you want in

Re: [gmx-users] Regarding version of gromacs

Thank you Justin for your suggestion As I run my simulation on supercomputer and there is availability of gromacs-5.1.2 version not 5.1.4. Earlier it had 5.1.4 version but now it has only 5.1.2 version. -- Ashma Khan Research Scholar Department of Chemistry AMU, Aligarh -- Gromacs Users mailing

Re: [gmx-users] pdb2gmx: Selecting Force Field in first command

On 4/10/20 9:03 PM, ferna...@hypernetlabs.io wrote: Hi all! Context I'm trying to run simple gromacs example commands below * gmx pdb2gmx -f 1aki.pdb -o 1aki_processed.gro -water spce * gmx pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc In a

[gmx-users] pdb2gmx: Selecting Force Field in first command

Hi all! Context I'm trying to run simple gromacs example commands below * gmx pdb2gmx -f 1aki.pdb -o 1aki_processed.gro -water spce * gmx pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc In a Docker container with a Dockerfile (Dockerfile = instruction

Re: [gmx-users] segmentation fault gmx do_dssp

On 4/10/20 8:07 PM, Sadaf Rani wrote: Dear Justin and Qinghua I am using gromacs 2020 for analysis and dssp version on my system is 2.2.1. Which version of dssp would be compatible with gromacs 2020? Your version should be fine, but make sure the dssp binary works properly on its own

Re: [gmx-users] segmentation fault gmx do_dssp

Dear Justin and Qinghua I am using gromacs 2020 for analysis and dssp version on my system is 2.2.1. Which version of dssp would be compatible with gromacs 2020? Qinghua, I am already using the stripped trajectory. Any suggestions would be appreciated. Thanks. Sadaf -- Gromacs Users mailing

[gmx-users] energy minimizing

hi friends I generated a box of mixed gas with gmx insert-moleculesI ran an energy minimizing.  the potential energy is 4.05e+07 and maximum force is 1.25e+03.I used different algorithm likes cg and steep for minimization. what do I have to do untill my system potential energy has negative

Re: [gmx-users] How to extend the force field by polariation parameters

On 4/10/20 6:44 PM, Zuzana Benkova wrote: Dear Justin, thank you for your answer. As I noticed, there is a model of Drude oscillators (shells) used in GROMACS to represent the polarization of atoms. However, there exists model of rigid rod dipole moment which, instead of oscillating

Re: [gmx-users] How to extend the force field by polariation parameters

Dear Justin, thank you for your answer. As I noticed, there is a model of Drude oscillators (shells) used in GROMACS to represent the polarization of atoms. However, there exists model of rigid rod dipole moment which, instead of oscillating distance between the core nucleus and the auxiliary

Re: [gmx-users] segmentation fault gmx do_dssp

On 4/10/20 5:48 PM, Sadaf Rani wrote: Dear Gromacs users I am doing an analysis of protein-ligand MD simulation of 150ns. I am trying to calculate secondary structure as below:- gmx do_dssp -f md_noPBC.xtc -s md.tpr -o ss.xpm -tu ns -dt 1 But I am getting segmentation fault error. Reading

Re: [gmx-users] segmentation fault gmx do_dssp

Hello, I guess the problem is about memory. You could strip the water and ions first, then process the striped trajectory. All the best, Qinghua On 4/10/20 11:48 PM, Sadaf Rani wrote: Dear Gromacs users I am doing an analysis of protein-ligand MD simulation of 150ns. I am trying to

[gmx-users] segmentation fault gmx do_dssp

Dear Gromacs users I am doing an analysis of protein-ligand MD simulation of 150ns. I am trying to calculate secondary structure as below:- gmx do_dssp -f md_noPBC.xtc -s md.tpr -o ss.xpm -tu ns -dt 1 But I am getting segmentation fault error. Reading file md.tpr, VERSION 2020-UNCHECKED (single

Re: [gmx-users] dt in mdp

On 4/10/20 4:17 PM, Alex wrote: On Fri, Apr 10, 2020 at 9:19 AM Justin Lemkul wrote: On 4/10/20 9:16 AM, Alex wrote: Thank you for the response. On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote: On 4/10/20 8:13 AM, Alex wrote: Dear Justin, Any comment please? Sorry, haven't had

Re: [gmx-users] dt in mdp

On Fri, Apr 10, 2020 at 9:19 AM Justin Lemkul wrote: > > > On 4/10/20 9:16 AM, Alex wrote: > > Thank you for the response. > > > > > > On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote: > > > >> > >> On 4/10/20 8:13 AM, Alex wrote: > >>> Dear Justin, > >>> Any comment please? > >> Sorry,

[gmx-users] Protonated ligand free energy calculation in water

Dear GROMACS users, I read and followed Dr. Lemkul's tutorial on Free Energy Calculation on the webpage, http://www.mdtutorials.com/gmx/free_energy/index.html It is very helpful and easy to follow, but my ligand is protonated so the atomic charges in the topol.top are non-zero. The

[gmx-users] Problem with pdb2gmx

Hi I want to simulate a protein which is bound covalently to a ligand. When I get the gro file of the complex the bond between the amino acid and the ligand is broken although I had modified the .rtp file before and it seems ok in a PDB format. In the topology, I got this warning message :

Re: [gmx-users] Problem with pdb2gmx

On 4/10/20 12:15 PM, Elham Taghikhani wrote: Hi I want to simulate a protein which is bound covalently to a ligand. When I get the gro file of the complex the bond between the amino acid and the ligand is broken although I had modified the .rtp file before and it seems ok in a PDB format.

Re: [gmx-users] GROMACS version issue

On 4/10/20 11:04 AM, Yasaman KARAMI wrote: Dear GROMACS developers, I am performing classical MD simulations of a membrane protein system, using GROMACS 2018.6 version. I have just noticed that after few nano seconds, the box dimensions are changing. Meaning that the system shrinks along

[gmx-users] GROMACS version issue

Dear GROMACS developers, I am performing classical MD simulations of a membrane protein system, using GROMACS 2018.6 version. I have just noticed that after few nano seconds, the box dimensions are changing. Meaning that the system shrinks along the z-axis, for example dimensions are changing

Re: [gmx-users] Regarding version of gromacs

On 4/10/20 9:21 AM, FAISAL NABI wrote: I have tried the same few days back but it didn't work. I have been using gromacs 2018.1 earlier and then switched to 5.1.4 and it didn't work. Switching between major versions that are years apart in their development will not work, and GROMACS has

Re: [gmx-users] Regarding version of gromacs

I have tried the same few days back but it didn't work. I have been using gromacs 2018.1 earlier and then switched to 5.1.4 and it didn't work. On Fri, Apr 10, 2020, 6:43 PM Ashma Khan wrote: > Dear all, > I have run my simulation on gromacs 5.1.4 for 200ns but now I want to > extend my

Re: [gmx-users] dt in mdp

On 4/10/20 9:16 AM, Alex wrote: Thank you for the response. On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote: On 4/10/20 8:13 AM, Alex wrote: Dear Justin, Any comment please? Sorry, haven't had power/network for a while due to some bad storms here. GROMOS force fields are

Re: [gmx-users] dt in mdp

Thank you for the response. On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote: > > > On 4/10/20 8:13 AM, Alex wrote: > > Dear Justin, > > Any comment please? > > Sorry, haven't had power/network for a while due to some bad storms here. > > GROMOS force fields are parametrized assuming all

[gmx-users] Regarding version of gromacs

Dear all, I have run my simulation on gromacs 5.1.4 for 200ns but now I want to extend my simulation to 500ns with gromacs 5.1.2. Is it possible or will there be problem during total simulation of 500ns in my systems. Please give me suggestion regarding this. -- Ashma Khan Research Scholar

Re: [gmx-users] Fwd: geometry optimization of metalloenzyme

On 4/9/20 4:25 PM, Nadia Elghobashi-Meinhardt wrote: Thank you, Justin. I am still struggling with constraints. I am trying to use "freezegrps" and "freezedim" to run an NVT equilibration. However, when I try to build the binary using my optimized structure, I get either "Segmentation fault"

Re: [gmx-users] dt in mdp

On 4/10/20 8:13 AM, Alex wrote: Dear Justin, Any comment please? Sorry, haven't had power/network for a while due to some bad storms here. GROMOS force fields are parametrized assuming all bonds are fixed, so your constraints should be "all-bonds" not "h-bonds." I would also suggest you

Re: [gmx-users] dt in mdp

Dear Justin, Any comment please? Regards, Alex On Tue, Apr 7, 2020 at 5:38 PM Alex wrote: > Thanks Justin for the response. > Please find below the mdp file. > The system is a thin film made out of a epoxy molecule, picture in be > below link, with water on top and bottom of the film. I even

Re: [gmx-users] Converting a tpr file to an older version of gromacs

Hi Paul, Thank you for your reply. In fact, there is the GMXPBSA tool but I still have errors with that too when I run it on the examples provided in the installation folder. I tried to seek some help but the developers aren't responding. Thank you anyway! - Mariem Le ven. 10 avr. 2020 à

[gmx-users] Fwd: Fwd: geometry optimization of metalloenzyme

Thank you, Justin. I am still struggling with constraints. I am trying to use "*freezegrps*" and "*freezedim*" to run an NVT equilibration of a structure (successfully geometry-optimized using freezegrps). However, when I try to build the binary using my optimized structure, I get either

Re: [gmx-users] Converting a tpr file to an older version of gromacs

Hello, there is no real supported way of doing this. You would need to re-create the TPR in the version you want to use it in. Can you use an external tool instead of g_mmpbsa that supports reading the newer file format? Cheers Paul On 09/04/2020 17:24, Mariem Ghoula wrote: Hi, I would

Re: [gmx-users] treating trajectory for diffusion calculations

Ah! am sorry, I figured out. Please ignore my mail. I was using wrong group selection for rmcomm in the command line. Sorry to all! Dave On Thu, Apr 9, 2020 at 11:26 PM Dave M wrote: > Hi All, > > I have a coarse-grained simulation box with water and oil phases. Just > playing with the

[gmx-users] treating trajectory for diffusion calculations

Hi All, I have a coarse-grained simulation box with water and oil phases. Just playing with the diffusion 'only on a single particle' (single martini coarse bead) gave me different results when I use -rmcomm on trajectories with and without -pbc nojump. NOTE: selected only single bead Same

[gmx-users] Buggy 2020?

Hello All, I am wondering if gromacs-2020 is buggy? or I am missing something?. In gromacs-2020, for a certain setup, I got following warning, WARNING: There are no atom pairs for dispersion correction But, for same system, gromacs-2019 does not give warning. Apparently, gromacs-2020 gives