Re: [gmx-users] Is Gromos force fields not recommended?

It is not like that...gromos is not compatible with gromacs... decission need to be taken depending on what system you want to simulate and what you are expecting from the simulation. On Tue 18 Feb, 2020, 6:27 AM Myunggi Yi, wrote: > Dear users, > > As the same as the title, > > Are Gromos force

Re: [gmx-users] Is Gromos force fields not recommended?

Hi, No. Why do you ask? Mark On Tue., 18 Feb. 2020, 01:57 Myunggi Yi, wrote: > Dear users, > > As the same as the title, > > Are Gromos force fields not recommended in Gromacs? > -- > Gromacs Users mailing list > > * Please search the archive at >

Re: [gmx-users] Keeping more than 1 version of gromacs on single os UBUNTU

Thank you, Sir! On Mon, Feb 17, 2020 at 8:16 PM Christian Blau wrote: > Hi Navneet, > > This is achieved by setting the installation directory with cmake for the > respective source code that you downloaded, then sourcing different GMXRC. > > Install different GROMACS builds fromt the source

[gmx-users] How to dynamically change the "pull-coord1-init" during SMD simulation

Hello everyone, This email is asking for some suggestions. Actually I'd like to conduct a kind of steered molecular dynamics simulation like this: Fixing one end of a protein, pulling the other end for a certain distance Δx (can be for example 0.5 nm, 0.2 nm ...), relaxing the whole system for

[gmx-users] Is Gromos force fields not recommended?

Dear users, As the same as the title, Are Gromos force fields not recommended in Gromacs? -- 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

Re: [gmx-users] Increase Graphene sheet size

genconf will only stack the box that you have in the original box in integer values. i.e. -nbox 2 4 10 If want a specific dimension, then the box you are stacking has to be an integer fraction of the final dimensions. Also note that the final dimension also has to be possible with the

[gmx-users] Fwd: Compiling with OpenCL for Macbook AMD Radeon Pro 560 GPU

Hello, I am trying to do the exact same as Michael in https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-February/124394.html but hit the exact same error of it not finding a simple header

[gmx-users] How to set restraints in free energy calculation?

Dear Gromacs users I am doing a free energy calculation of the protein-ligand complex. During decoupling of the ligand vdw forces from protein, I have selected 21 different lambda windows between 0-1. I have put distance angle and dihedral restraints to keep the ligand in its position but in some

Re: [gmx-users] REMD stall out

Thanks Mark and Szilard, I forwarded Mark's suggestion to IT. I'll see what they have to say and then I'll try the simulation again and open an issue on redime. Thank you, Dan On Mon, Feb 17, 2020 at 9:09 AM Mark Abraham wrote: > Hi, > > That could be caused by configuration of the parallel

Re: [gmx-users] REMD stall out

Hi, That could be caused by configuration of the parallel file system or MPI on your cluster. If only one file descriptor is available per node to an MPI job, then your symptoms are explained. Some kinds of compute jobs follow such a model, so maybe someone optimized something for that. Mark On

Re: [gmx-users] REMD stall out

Hi Dan, What you describe in not an expected behaviro and it is something we should look into. What GROMACS version were you using? One thing that may help diagnosing the issue is: try to disable replica exchange and run -multidir that way. Does the simulation proceed? Can you please open an

Re: [gmx-users] REMD stall out

HI Szilard, I've deleted all my output but all the writing to the log and console stops around the step noting the domain decomposition (or other preliminary task). It is the same with or without Plumed - the TREMD with Gromacs only was the first thing to present this issue. I've discovered

Re: [gmx-users] Keeping more than 1 version of gromacs on single os UBUNTU

Hi Navneet, This is achieved by setting the installation directory with cmake for the respective source code that you downloaded, then sourcing different GMXRC. Install different GROMACS builds fromt the source code into seperate folders using something like

[gmx-users] CGENFF validation / optimization

Dear all, While suing CGENFF server for " *.str " file generation, Few of the penalties were found to higher than 50. How to do validation/optimization.? Is there any recommended softwares / servers available for * " extensive validation / optimization." or any standard procedure available to do

Re: [gmx-users] (no subject)

Thanks christian for the detailed description. On Mon, Feb 17, 2020 at 8:00 PM Christian Blau wrote: > Hi Shakkira, > > > The simulation box deformation is described by six parameters that > describe three basis box vectors with the following > contraints, > > - the first box vector is

Re: [gmx-users] (no subject)

Hi Shakkira, The simulation box deformation is described by six parameters that describe three basis box vectors with the following contraints,  - the first box vector is aligned along the x-axis, with coordinates thus has coordinates (xx,0,0)  - the second box vector is aligned in the x-y

[gmx-users] Keeping more than 1 version of gromacs on single os UBUNTU

Hello Everyone! I have currently installed GROMACS 2018.8 and using it. But for some of my previous work, I want to use the older version of GROMACS i.e 5.x. I have installed the GROMACS using this method >sudo cmake .. -DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=OFF

Re: [gmx-users] REMD stall out

Hi, If I understand correctly your jobs stall, what is in the log output? What about the console? Does this happen without PLUMED? -- Szilárd On Tue, Feb 11, 2020 at 7:56 PM Daniel Burns wrote: > Hi, > > I continue to have trouble getting an REMD job to run. It never makes it > to the point

Re: [gmx-users] Protein-Ligand Interaction calculation

On 2/17/20 7:18 AM, Peter Mawanga wrote: Hello everyone I used the CHARMM-GUI Membrane Builder to build a bilayer around my protein-ligand complex. However, unfortunately the ligand was not mentioned separately in the index (.ndx) file although it was mentioned in the topology (.top) file.

Re: [gmx-users] Protein-Ligand Interaction calculation

Hi.. You have to specify energy groups in .mdp option..then rerun the simulation..and analyse with gmx energy command On Mon 17 Feb, 2020, 5:52 PM Александр Лашков, wrote: > You can rebuild index file using gmx make_ndx gromacs util. > Alex > > пн, 17 февр. 2020 г. в 15:19, Peter Mawanga

Re: [gmx-users] Protein-Ligand Interaction calculation

You can rebuild index file using gmx make_ndx gromacs util. Alex пн, 17 февр. 2020 г. в 15:19, Peter Mawanga : > Hello everyone > > I used the CHARMM-GUI Membrane Builder to build a bilayer around my > protein-ligand complex. > > However, unfortunately the ligand was not mentioned separately in

[gmx-users] Protein-Ligand Interaction calculation

Hello everyone I used the CHARMM-GUI Membrane Builder to build a bilayer around my protein-ligand complex. However, unfortunately the ligand was not mentioned separately in the index (.ndx) file although it was mentioned in the topology (.top) file. Hence I am not able to calculate the energy

[gmx-users] Increase Graphene sheet size

Hello All, I want to create a graphene sheet with a specific dimensions (10*15*0.284) nm. I created a .gro file as below ( as mentioned in this website https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/ ) GRM: 1 1

Re: [gmx-users] syntax error in GMXRC.csh in Gromacs2020

Hello, Please open an issue on redmine for this. Cheers Paul On Mon, 17 Feb 2020, 10:07 Harry Mark Greenblatt, < harry.greenbl...@weizmann.ac.il> wrote: > BS”D > > Seems that a bash formatted line has made it into the csh version of the > GMXRC file: > > setenv

Re: [gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output

Hi, I guess that the reported energy are averaged over the simulation time. If you want to compare energies and understand what change in the topology implied, it is better to compare the energies of the first step using the same starting structure. The definition of LJ interactions (including

[gmx-users] syntax error in GMXRC.csh in Gromacs2020

BS”D Seems that a bash formatted line has made it into the csh version of the GMXRC file: setenv GMXTOOLCHAINDIR=${GMXPREFIX}/share/cmake The “=“ should be a space. Harry Harry M. Greenblatt Associate Staff Scientist

Re: [gmx-users] Cannot flush logfile - maybe you are out of disk space?

Hi, On Mon, Feb 17, 2020 at 7:48 AM Dilip.H.N wrote: > Dear all, > I have extended a simulation (extension for 50 ns) and after some time i > get the following error "Cannot flush logfile - maybe you are out of disk > space?" and now the simulation has stopped running. The log file of the >

Re: [gmx-users] Tabulated potentials

Hi, On Fri, Feb 14, 2020 at 5:17 PM Ali Khodayari < ali.khoday...@student.kuleuven.be> wrote: > Thank you Alessandra. However, fixing the topology did not remove the > error. It still stands as before: > > A tabulated bond interaction table number 4 is out of the table range: r > 0.575410,