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 > this

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 us

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 http://www.gromacs.org/Suppo

[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 input:

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 av

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 for

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 tripl

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 > > https://devblogs.nvidia.com/creating-faster-m

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: cann

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 N-acet

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. pull_coord1_group

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? Wh

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 fr

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* Dip

[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 hydrog

[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? bec

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 i