Re: [gmx-users] Fwd: setting ionic liquid simulation in gromacs

Hi What error you are getting? On Fri 20 Dec, 2019, 1:14 PM Devargya Chakraborty, < devargyachakraborty@gmail.com> wrote: > -- Forwarded message - > From: Devargya Chakraborty > Date: Thu, 19 Dec 2019 at 18:17 > Subject: setting ionic liquid simulation in gromacs > To:

Re: [gmx-users] Extract LJ-14 energy

On 12/20/19 6:07 AM, Suvardhan Jonnalagadda wrote: Hi, Thanks for the reply. I have included it and rerun my system. Still problem prevails. energrps are not required for LJ 1-4 energies, as these are intramolecular and energygrps correspond strictly to intermolecular interaction

[gmx-users] GROMACS 2020 release candidate

Hi GROMACS users, The GROMACS 2020 release candidate is now out and available! As before, we are making the testing versions available for you to be able to get feedback on how well things are working, and what could be improved or if there are any bugs in the code we have missed ourselves.

[gmx-users] definition of the prefactors in the wall potentials

Dear gmx-users, I am looking for the explicit formula of the wall potentials implemented when one uses the wall mdp options. In the gromacs user-guide, there are indications on the dependence relative to the distance z to the wall : for example LJ 9-3, I understand it is a sum of a

[gmx-users] restraints

Dear Gromacs users I want to run free energy calculation of a protein-ligand complex by putting distance, angle and dihedral restraints between ligand and protein. Before that, I run 1ns MD (without free energy input) in order to know that my ligand restraints are working well or otherwise.

Re: [gmx-users] Extract LJ-14 energy

Hi, I am facing the same issue in version 5.1.4 as well. I have 1-4 interactions in my system (mentioned 'gen-pair' yes in 'forcefield.itp file) Is there a way to extract the 1-4 interaction energy? Thank you On Fri, Dec 20, 2019 at 2:43 PM Mark Abraham wrote: > Hi, > > On Thu., 19 Dec.

Re: [gmx-users] [solved] Can't engage OpenCL (No rule to make target /usr/lib/libOpenCL.so)

The problem has been solved by installing ocl-icd-opencl-dev. I think this package should be mentioned in the installation guide. 19.12.2019, 01:20, "Mark Abraham" :Hi,If you use -DOpenCL_LIBRARY then it has to indicate the location oflibOpenCL.so because you've short-circuited any attempt to find

Re: [gmx-users] Gromacs compilation problem

Hi, The fftw build you are trying to do uses gcc by default, and your gcc is so old that AVX512 didn't exist yet, so it cant compile for it. Since you're using the Intel compiler, it's easiest to also use its fft library with cmake -DGMX_BUILD_OWN_FFTW=OFF -DGMX_FFT_LIBRARY=mkl Harder is to

Re: [gmx-users] CO2 virtual site

Hi, On Fri., 20 Dec. 2019, 09:59 Sina Omrani, wrote: > Hi, > I have a problem when I use CO2 model with virtual sites during energy > minimization. I used itp file in the md tutorial and beside the fact that > some of my water molecules can not be settled, I get a positive potential > energy

Re: [gmx-users] Extract LJ-14 energy

Hi, On Thu., 19 Dec. 2019, 18:41 Suvardhan Jonnalagadda, wrote: > Hi All, > > *"GROMACS: VERSION 4.5.5; Precision: single"* > This software is nearly a decade old and is no longer supported. Please update. I have performed an md simulation for 1 time step, on a single molecule > with 17

[gmx-users] CO2 virtual site

Hi, I have a problem when I use CO2 model with virtual sites during energy minimization. I used itp file in the md tutorial and beside the fact that some of my water molecules can not be settled, I get a positive potential energy and high force on molecules. Is something wrong? And another

Re: [gmx-users] segmantation fault

Hi, Maybe the nvt.log file provides you more information on the problem Best regards Alessandra On Fri, Dec 20, 2019 at 9:40 AM Bratin Kumar Das < 177cy500.bra...@nitk.edu.in> wrote: > Dear all, > During running nvt equilibration I got the following error. > gmx mdrun -v -s

Re: [gmx-users] constraints

Hi On Thu, Dec 19, 2019 at 3:41 PM Maria Luisa wrote: > Dear users, > I want to constraints a group of molecules inside a tri-layer structure. > How can I label and fix these molecules ? > > Depends on the problems, but to fix atoms to a reference position, you can use position restraints (

[gmx-users] segmantation fault

Dear all, During running nvt equilibration I got the following error. gmx mdrun -v -s nvt.tpr -deffnm nvt -cpi nvt.cpt -append :-) GROMACS - gmx mdrun, 2016.5 (-: GROMACS is written by: Emile Apol Rossen Apostolov Herman