Re: [gmx-users] OPLS parameters for O2

Den 2019-05-10 kl. 00:42, skrev Shadi Fuladi: Hi, I'm trying to test molecular oxygen diffusion in electrolytes using OPLS force field. Is there any O2 parameters tested with OPLS AA forcefield? Thanks, SF There is a model described here Hub, J. S.; de Groot, B. L. Proc. Natl. Acad. Sci.

Re: [gmx-users] Gromacs 2019.2 on Power9 + Volta GPUs (building and running)

Yup, your assessment agrees with our guess. Our HPC guru will be taking his findings, along with your quote, to the admins. Thank you, Alex On Thu, May 9, 2019 at 2:51 PM Szilárd Páll wrote: > On Thu, May 9, 2019 at 10:01 PM Alex wrote: > > > Okay, we're positively unable to run a Gromacs

[gmx-users] OPLS parameters for O2

Hi, I'm trying to test molecular oxygen diffusion in electrolytes using OPLS force field. Is there any O2 parameters tested with OPLS AA forcefield? Thanks, SF -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] Gromacs 2019.2 on Power9 + Volta GPUs (building and running)

On Thu, May 9, 2019 at 10:01 PM Alex wrote: > Okay, we're positively unable to run a Gromacs (2019.1) test on Power9. The > test procedure is simple, using slurm: > 1. Request an interactive session: > srun -N 1 -n 20 --pty > --partition=debug --time=1:00:00 --gres=gpu:1 bash > 2. Load CUDA

Re: [gmx-users] Gromacs 2019.2 on Power9 + Volta GPUs (building and running)

Okay, we're positively unable to run a Gromacs (2019.1) test on Power9. The test procedure is simple, using slurm: 1. Request an interactive session: > srun -N 1 -n 20 --pty --partition=debug --time=1:00:00 --gres=gpu:1 bash 2. Load CUDA library: module load cuda 3. Run test batch. This starts

[gmx-users] charge density of multiple frames in a limited region

Dear Users, In using: gmx density -f lipid.nvt.trr -s octanoate.nvt3.tpr -dens charge -center -symm -sl 100 -b 4 -e 4.5 it appears that the average charge density of all frames and the total box size is used in the calculation. Is there a way to 1) specify multiple ranges to output say, every

[gmx-users] mdrun log file question

hello all,I am running an md simulation using gromacs 2019 with RDC restraints added in all steps, now in my log file i get something like this Orientation experiment 1:     order parameter: -0.00156791     eig:  1.000   -0.085  0.037  0.996     eig: -0.636   -0.144  0.988 -0.049     eig: -0.364 

Re: [gmx-users] TIP4P molecules stuck together

Dr. Shirts, Thank you for the swift reply. > If you have "unprotected" electrostatic sites (i.e. with nonzero repulsive > terms directly on top of the charge), then there will always be some > configurations with essentially infinitely negative energy. That makes sense. Definitely something to

Re: [gmx-users] TIP4P molecules stuck together

If you have "unprotected" electrostatic sites (i.e. with nonzero repulsive terms directly on top of the charge), then there will always be some configurations with essentially infinitely negative energy. For vanilla MD, these are essentially impossible to reach kinetically at any reasonable

[gmx-users] TIP4P molecules stuck together

Hi all, I have a rather strange question that I hope someone can shed some light on. Before I begin, I want to note that I am pioneering some new developments of the Adaptive Resolution Simulation technique (https://doi.org/10.1002/adts.201900014), so the simulations/techniques I am

[gmx-users] dipole moment of water using TIP3P model

Dear Users, It is known that electric dipole moment of a water monomer is experimentally 1.85 D and using the TIP3P model it's supposed to be 2.35D. I am using the TIP3P model for a water-based simulation in Gromacs 5.1.5. After applying sinusoidal electric fields in the Y axis, the norm of the

Re: [gmx-users] ligand in water

This will do it (if need particular water model change with cs switch options, and assumes ligand.gro has the correct final box size) gmx solvate - cp ligand.gro -cs -o complex.gro Unless you have a particular number of waters required, then use.: gmx solvate - cp ligand.gro -cs -o complex.gro

[gmx-users] ligand in water

Hi Users. I want to simulate ligand in the water box. I prepared a water molecule and started with pdb2gmx and then planned to follow protein-ligand tutorial. Unfortunately ended up with an error in gro file format. Have check every possibility but still couldn't find any solution. My initial pdb

Re: [gmx-users] gmx hbond query

Make index of water mediated hydrogens and DNA bases so that DNA bases are in separate group and water mediated hydrogens in separate group in drop down menu On Thu, May 9, 2019, 11:54 AM wrote: > Dear all > I want to determine the water mediated hydrogen between DNA bases and > small molecule.

Re: [gmx-users] Gromacs2018.5 install with gaussian09 for QM/MM

Hi, I think it will still work if you use the "gau": script found here: http://wwwuser.gwdg.de/~ggroenh/qmmm.html#gaussian best, Gerrit On 5/7/19 9:59 PM, ??? wrote: > Dear Gromacs support, > I want to install Gromacs 2018.5 with gaussian09 software support in Centos > system, I try to

[gmx-users] gmx hbond query

Dear all I want to determine the water mediated hydrogen between DNA bases and small molecule. What extra flag should I use in gmx hbond command? Is there any other option to capture the water mediated Hbonds? Please suggest something. Sunipa Sarkar -- Gromacs Users mailing list * Please

Re: [gmx-users] Implicit Solvent with User Defined Potentials

Den 2019-05-08 kl. 16:21, skrev Akash Banerjee: Dear Gromacs Developer, I want to use the implicit solvent (gbsa algorithm) along with User-defined tabulated potentials. Apparently, the implicit solvent option is not compatible with the vdw-type=USer option. Can I please get some advice on