Re: [gmx-users] GROMACS 2020.1 failed to pass make check

Hi Paul, Thank you so much for your reply! That is very helpful. Best, Wei-Tse On Mon, Apr 6, 2020 at 1:23 AM Paul bauer wrote: > Hello, > > you are using a plumed modified version that adds extra options to mdrun. > Our unit tests check that the output from mdrun -h stays invariant, and >

Re: [gmx-users] How to parametrize a new molecule?

Thanks, Mahdi. I'm aware of that study. Actually it's because of it that I have chosen the latest CHARMM27 for the simulations. Best, Herbert Em sáb., 4 de abr. de 2020 às 12:57, Mahdi Bagherpoor escreveu: > Hello Herbert, > > Not related to your question, but be careful if you are going to

Re: [gmx-users] Velocities from the .gro file

On 4/6/20 12:16 PM, Mohamed Abdelaal wrote: Hello everybody :) Can I use the gmx insert-molecules to insert molecules in my box with velocities by adding the velocities in the .gro file and insert the molecules from this .gro file ? Have you tried it? -Justin --

[gmx-users] Velocities from the .gro file

Hello everybody :) Can I use the gmx insert-molecules to insert molecules in my box with velocities by adding the velocities in the .gro file and insert the molecules from this .gro file ? Thanks Mohamed -- Gromacs Users mailing list * Please search the archive at

[gmx-users] restarting a simulation

Dear Gromacs users I am restarting a simulation with the following command:- mpirun gmx_mpi mdrun -s md10.tpr -cpi md10_prev.cpt -append However, I am getting following error message. All the below-named files are there in my directory but it still complains the same. Inconsistency in user

Re: [gmx-users] Fumbling in the dark with dihedral pulling

On 4/6/20 10:53 AM, Marko Petrovic wrote: Thank you. I updated the mdp file. (Is the dihedral defined as a pair of planes rather than a triplet of vectors?) Perhaps my interpretation of the documentation was incorrect; I thought the planes were supposed to be defined, but I suppose it's

Re: [gmx-users] Fumbling in the dark with dihedral pulling

Thank you. I updated the mdp file. (Is the dihedral defined as a pair of planes rather than a triplet of vectors?) Unfortunately I still get the segmentation fault and similar warnings. I will try to compile the differences between the sample mdp and the one I used, then see which differences

[gmx-users] Anharmonic/Morse flexible water

Hi all, I am currently trying out various water models for some solute/solvent systems and I was wondering if there are any (reliable) anharmonic/Morse flexbile water models that can be used in Gromacs? I've seen that can set [ Morse ] for bonds, but don't want to start doing random changes to

Re: [gmx-users] Bonds definition in itp files

On 4/6/20 9:55 AM, Sina Omrani wrote: Thanks, dear Justin. if I define a constraint on a bond then force constant isn't useless? Yes, because you no longer have a harmonic interaction. It is a fixed length. Whether or not the bond should be constrained is dictated by whether or not the

Re: [gmx-users] Bonds definition in itp files

Thanks, dear Justin. if I define a constraint on a bond then force constant isn't useless? On Mon, 6 Apr 2020 at 17:12, Justin Lemkul wrote: > > > On 4/6/20 7:24 AM, Sina Omrani wrote: > > Hi, > > I wanted to know how we specify a bond order in our simulation? For > > example, if we have a

Re: [gmx-users] Multi-GPU optimization, "DD without halo exchange is not supported"

On Fri, Mar 27, 2020 at 8:30 PM Leandro Bortot wrote: > Dear users, > > I'm trying to optimize the execution of a system composed by 10 > million atoms on a multi-GPU machine with GROMACS 2020.1. > I've followed the instructions given at > >

Re: [gmx-users] Unable to compile GROMACS 2020.1 using GNU 7.5.0

On Sat, Apr 4, 2020 at 10:41 PM Wei-Tse Hsu wrote: > Dear gmx users, > Recently I've been trying to install GROMACS 2020.1. However, I encounter a > compilation error while using the make command. The error is as follows: > > > > > > */usr/bin/ld: cannot find /lib/libpthread.so.0/usr/bin/ld:

Re: [gmx-users] NAG N-Acetylglucosamine force field parameters

Dear Javier, The way GROMOS force fields are parameterized allows building blocks to be linked together and still provide a good model. You can find parameters for glucose in the force field (in the aminoacids.rtp file) and from there on, you only need to find adequate parameters for the

Re: [gmx-users] Fumbling in the dark with dihedral pulling

On 4/6/20 2:33 AM, Marko Petrovic wrote: I figure it might be helpful to see my other files so I include a link: https://github.com/SpaceDucK77/StringMethodMaster/tree/master/Prototypes/P3_Pull_coordinates/manual_test_justin Your dihedral definitions are simply incorrect.

Re: [gmx-users] Bonds definition in itp files

On 4/6/20 7:24 AM, Sina Omrani wrote: Hi, I wanted to know how we specify a bond order in our simulation? For example, if we have a triple bond in our structure between atoms 1 and 2, is it by length and force constants or we define 1 and 2 bonds three times in the bond section of itp file?

Re: [gmx-users] Protonation state of aminoacids from pdb and pdb2gmx

On 4/6/20 8:10 AM, Javier Luque Di Salvo wrote: Dear Gromacs users, I'm aware that there might be plenty of discussions on this matter, anyway I would like to get your advice. Which is the proper way to know the protonation state that is generated with pdb2gmx? I have downloaded a pdb file

Re: [gmx-users] NAG N-Acetylglucosamine force field parameters

Dear Javier, NAG is surely available in the GLYCAM library, an AMBER-based force field. Pay attention to the scaling factors when you use GLYCAM force field, especially if you use it with other AMBER-based FF (which are mutually compatible) in GROMACS. Best, Tommaso

[gmx-users] NAG N-Acetylglucosamine force field parameters

Dear Gromacs users, Do you know where can I search for force field parameters of N-Acetylglucosamine (NAG)? I'm interested in AMBER, CHARMM and GROMOS force fields, my Gromacs version is 2018.3 Thanks in advance, Javier -- *Javier Luque Di Salvo*

[gmx-users] Protonation state of aminoacids from pdb and pdb2gmx

Dear Gromacs users, I'm aware that there might be plenty of discussions on this matter, anyway I would like to get your advice. Which is the proper way to know the protonation state that is generated with pdb2gmx? I have downloaded a pdb file from the Protein Data Bank. The structure has no

[gmx-users] Bonds definition in itp files

Hi, I wanted to know how we specify a bond order in our simulation? For example, if we have a triple bond in our structure between atoms 1 and 2, is it by length and force constants or we define 1 and 2 bonds three times in the bond section of itp file? What if we use a constraint on this bond?

Re: [gmx-users] GROMACS 2020.1 failed to pass make check

Hello, you are using a plumed modified version that adds extra options to mdrun. Our unit tests check that the output from mdrun -h stays invariant, and this is no longer the case once you modify the code for plumed. You can ignore this failure in this case, but please mention in the future

Re: [gmx-users] Fumbling in the dark with dihedral pulling

I figure it might be helpful to see my other files so I include a link: https://github.com/SpaceDucK77/StringMethodMaster/tree/master/Prototypes/P3_Pull_coordinates/manual_test_justin With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and