Re: [gmx-users] How to reduce the penalty of small molecule from CGenFF

Hello Justin, Thank you and yes. I went to the paper and it shows the steps for optimization. However, I have the following problems as I tried to follow the tutorial on CGenFF page, http://mackerell.umaryland.edu/~kenno/cgenff/download.php#tutor (1) what are these parameters in water_constr.inp?

[gmx-users] Thin film drifting

Dear all, In a system, I have a thin_film (infinitive in x-y directions) with water on top and bottom of it, PBC = xyz. By the below flags I try to remove the motion of the center of mass of the two group separately. comm-grps = thin_film Water comm-mode = Linear nstcomm = 100

Re: [gmx-users] replica exchange simulations performance issues.

correction: 99.3% is going into NxN Ewald Elec. + LJ [F] On Sun, Mar 29, 2020 at 12:55 PM Miro Astore wrote: > > Hi everybody. I've been experimenting with REMD for my system running > on 48 cores with 4 gpus (I will need to scale up to 73 replicas > because this is a complicated system with

[gmx-users] replica exchange simulations performance issues.

Hi everybody. I've been experimenting with REMD for my system running on 48 cores with 4 gpus (I will need to scale up to 73 replicas because this is a complicated system with many DOF I'm open to being told this is all a silly idea). My run configuration is mpirun -np 4 --map-by numa gmx_mpi

Re: [gmx-users] Various questions related to Gromacs performance tuning

On Sat, Mar 28, 2020, at 9:32 PM, Kutzner, Carsten wrote: > > > > Am 26.03.2020 um 17:00 schrieb Tobias Klöffel : > > > > Hi Carsten, > > > > > > On 3/24/20 9:02 PM, Kutzner, Carsten wrote: > >> Hi, > >> > >>> Am 24.03.2020 um 16:28 schrieb Tobias Klöffel : > >>> > >>> Dear all, > >>> I

Re: [gmx-users] Various questions related to Gromacs performance tuning

> Am 26.03.2020 um 17:00 schrieb Tobias Klöffel : > > Hi Carsten, > > > On 3/24/20 9:02 PM, Kutzner, Carsten wrote: >> Hi, >> >>> Am 24.03.2020 um 16:28 schrieb Tobias Klöffel : >>> >>> Dear all, >>> I am very new to Gromacs so maybe some of my problems are very easy to fix:) >>> Currently

Re: [gmx-users] Per atom energies

Den 2020-03-28 kl. 04:01, skrev Guilherme Carneiro Queiroz da Silva: Hi all, I look on google for any answers for such question in this maillist, and I found related questions but no final answer. I wish to compute the heat flux for my system using GK relations. I found the gromacs extension

Re: [gmx-users] SARS-CoV-2 main protease with ligand from acpype, but converting to vsites?

Hi Bjorn (and others interested in virtual sites for non-protein molecules), We have an article in press where we describe our new tool Mkvsites, which is a great help when you want virtual sites for a new residue, ligand, etc. I will announce the article once it is available, but I might as

Re: [gmx-users] Per atom energies

Hi, On Sat., 28 Mar. 2020, 04:04 Guilherme Carneiro Queiroz da Silva, < gcarnei...@pos.iq.ufrj.br> wrote: > Hi all, > > I look on google for any answers for such question in this maillist, and I > found related questions but no final answer. > > I wish to compute the heat flux for my system