Re: [gmx-users] Umbrella Sampling - Changing force constant values between samples

On 10/22/18 1:45 PM, Dan Gil wrote: Hello, I am wondering if it is valid to use different force constant (k) values between samples for umbrella sampling. It seems that gmx_wham accepts different k values in a set, but I wanted to make sure this is OK. Should I be wary of any artifacts with

[gmx-users] Umbrella Sampling - Changing force constant values between samples

Hello, I am wondering if it is valid to use different force constant (k) values between samples for umbrella sampling. It seems that gmx_wham accepts different k values in a set, but I wanted to make sure this is OK. Should I be wary of any artifacts with these simulations? Best Regards, Dan

Re: [gmx-users] First beta release of 2019

Hello GROMACS users, the correct link to the release notes is here: http://manual.gromacs.org/documentation/2019-beta1/release-notes/index.html Cheers Paul Bauer GROMACS Release manager On 22/10/2018 17:29, Paul bauer wrote: Hi GROMACS users, The first beta release of GROMACS 2019 is

[gmx-users] First beta release of 2019

Hi GROMACS users, The first beta release of GROMACS 2019 is available! We are making this available to you to get an early taste of how GROMACS 2019 will look and work, and most importantly to get feedback from you about how well things work. While we try our hardest to keep the quality of

Re: [gmx-users] numerical reproducibility on Gromacs 2018.3 GPU

Hi, On Mon, Oct 22, 2018 at 1:36 PM Hubert Santuz wrote: > Hi, > > Thanks for your response and the link to the documentation. I missed that > :) > The non-deterministic order is due to the fact that the sum of the NB terms > in GPU kernels is done "independently" and leads to a different order

[gmx-users] GLYCAM for gromacs

Dear gmx users, We are trying to simulate polysaccharides, cellulose and hemicellulose in particular, in GROMACS. The intention is to use GLYCAM forcefield parameters as well. My question is, is there any properly quick way to parametrize GLYCAM force field to be used in GROMACS?

Re: [gmx-users] Turn on/off residues in gromacs

On 10/22/18 7:29 AM, Quyen Vu Van wrote: Dear all, sorry for my unclear question, I attached here the quick draw picture of what I am saying, please take a look: https://www.dropbox.com/s/eycsm3qsywhgxjv/model.pdf?dl=0 What you are trying to do is both technically challenging and physically

Re: [gmx-users] numerical reproducibility on Gromacs 2018.3 GPU

Hi, Thanks for your response and the link to the documentation. I missed that :) The non-deterministic order is due to the fact that the sum of the NB terms in GPU kernels is done "independently" and leads to a different order of the sum ? Am I reading correctly ? Can we compare it, more or less,

Re: [gmx-users] Turn on/off residues in gromacs

Dear all, sorry for my unclear question, I attached here the quick draw picture of what I am saying, please take a look: https://www.dropbox.com/s/eycsm3qsywhgxjv/model.pdf?dl=0 Thank you and best regards, Quyen On Sat, Oct 20, 2018 at 6:27 AM Quyen Vu Van wrote: > Dear Mark, > I mean that e.g

Re: [gmx-users] numerical reproducibility on Gromacs 2018.3 GPU

Hi, On Mon, Oct 22, 2018 at 11:11 AM Hubert Santuz wrote: > Hi everyone, > > I'm trying to get numerical identical results on a test system (di-alanine > in water) with Gromacs 2018.3 version with GPU. I'm doing 100 steps in NVE. > > When I'm using GPU (gmx mdrun -nt 1 -nb gpu), I'm not getting

[gmx-users] numerical reproducibility on Gromacs 2018.3 GPU

Hi everyone, I'm trying to get numerical identical results on a test system (di-alanine in water) with Gromacs 2018.3 version with GPU. I'm doing 100 steps in NVE. When I'm using GPU (gmx mdrun -nt 1 -nb gpu), I'm not getting exactly the same results when I launch 2 separated times the same