Re: [gmx-users] how to run equilibration when freezing part of an small molecule in vacuum and in water environment?

On 4/13/20 10:37 AM, lazaro monteserin wrote: Dear Gromacs users I have three questions about the details of running MD of small molecules in gromacs: 1) If I run a MD in vacuum if I freeze part of the nucleoside (lets say the carbons in the sugar) with genrestr, should I use temperature

Re: [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs

Thank you very much Neena. I will try these parameters. Kindly, Lazaro El dom., 12 de abr. de 2020 a la(s) 23:53, Neena Susan Eappen ( neena.susaneap...@mail.utoronto.ca) escribió: > Try the below minim.mdp parameters which has worked well for vacuum > simulations. Proper way to do vacuum

[gmx-users] how to run equilibration when freezing part of an small molecule in vacuum and in water environment?

Dear Gromacs users I have three questions about the details of running MD of small molecules in gromacs: 1) If I run a MD in vacuum if I freeze part of the nucleoside (lets say the carbons in the sugar) with genrestr, should I use temperature coupling groups? 2) Now, if I freeze in the

[gmx-users] energy minimization

hi friends I generated a box of mixed gas with gmx insert-moleculesI ran an energy minimizing.  the potential energy is 4.05e+07 and maximum force is 1.25e+03.I used different algorithm likes cg and steep for minimization. what do I have to do untill my system potential energy has negative

[gmx-users] Basic question about command line

Dear all Hi, I have a basic question about the using the gromacs. I want to use gmx cluster for clustering. I use the cluster hpc. When I run the this command: gmx cluster -f *.trr -s *.gro -g *.log -clid *.xvg I receive the error that I should select the group for least rmsd. Could you please

Re: [gmx-users] Replica exchange probabilities beyond version 2016

Hi Pritam, Did you check your energy fluctuations? Looks like you are using NH thermostat, you might be suffering from the interaction of NH thermostat oscillations with resonance modes in the system, which makes energy fluctuations substantially larger (compared to fluctuations with NH in older

[gmx-users] Replica exchange probabilities beyond version 2016

Hello, I have noticed that the average exchange probability for a replica exchange run increases significantly if I use Gromacs versions 2018, as compared to versions 2016 or earlier. I have tested that by simulating the same system with versions 2016.4 and 2018.3 and the average

[gmx-users] Ways to calculate shear viscosity

Hi all, I have sent this before but no one answers. I want to simulate a couvette flow using gromacs by applying a deform velocity at xz direction. For a pure water box, it works well though there are warnings "the box is too skewed". When I put a surfactant micelle in the middle, that warning

Re: [gmx-users] how to run equilibration when freezing part of an small molecule in vacuum and in water environment?

Dear Dr. Lemkul thank you very much for your answer. I will look on the literature. El lun., 13 de abr. de 2020 a la(s) 12:55, Justin Lemkul (jalem...@vt.edu) escribió: > > > On 4/13/20 10:37 AM, lazaro monteserin wrote: > > Dear Gromacs users > > > > I have three questions about the details of

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

Dear Szilárd, Thank you for your answer. I'm already exporting the three variables as separate commands (maybe what you saw was some formatting problem with the email? I'm not sure). For clarity, I just tested the following line: export GMX_GPU_DD_COMMS=true ; export

[gmx-users] Polarization assistance request

Hello GROMACS Users, I was wondering if anyone who has experience with simulations using polarization would be willing to take a look at what I’ve tried that so far hasn’t worked and give some tips and perhaps share their topology files and run settings. I am attempting to model a 3-atom

[gmx-users] Error message

Hi, I am simulating a water droplet in gas phase using Gromacs. Basically, this is a water droplet kept at the centre of a large box of dimension 100 nm. The problem is that the run ended with an error message as shown below: “8 particles communicated to PME rank 14 are more than 2/3 times

Re: [gmx-users] Problem with pdb2gmx

On 4/12/20 2:42 PM, Elham Taghikhani wrote: Hi Yes the spacbond.dat and residuetypes.dat files are in my oplsa folder in my working directory. These files should be in the working directory, not in the force field subdirectory. This is why they are not being read. When it gives me