Re: [gmx-users] GROMACS mailing-list will move to a forum

Hello gmx users! As announced in my previous message at the beginning of the week, we will be activating the new discussion forum today. At the same time, the mailing list will move to read-only mode, so please don't be surprised when it is no longer possible to submit new messages to it.

[gmx-users] Question about parameters for simulation annealing

Dear Gromacs users, I am trying to run a simulation annealing using Gromacs of a small molecule. Does anybody knows if there is a protocol to set up the annealing parameters for Gromacs; initial temperature, final temperature, annealing-npoints, annealing-ntimes and the annealing-temp? My total

Re: [gmx-users] gmx distance com error

Cs : : : : : / **:***/

[gmx-users] Negative part of the reaction coordinate in PMF

Dear all, In a PMF simulation using WHAM, the windows are somehow that the reaction coordinate (RC = COM_group1 COM_group2) should have both positive and negative parts along Z direction, e.g COM_group1 locates in the middle of the reaction coordinate more or less. However, what the WHAM

[gmx-users] gmx distance com error

Hello gmx users, I am stuck at a very basic command line and need your expertise in dealing through it. Basically, I have a clay sheet containing 192 surface oxygen. Since I am doing umbrella sampling for PMF calculations, I want to get the progression of COM distances of my fixed Cs atom from

Re: [gmx-users] How to apply position restrain on selected atoms in .gro files in Gromacs?

Hello gmx users, I am stuck at a very basic command line and need your expertise in dealing through it. Basically, I have a clay sheet containing 192 surface oxygen. Since I am doing umbrella sampling for PMF calculations, I want to get the progression of COM distances of my fixed Cs atom from

Re: [gmx-users] Question on energygrps setting

On 5/7/20 10:57 AM, Devargya Chakraborty wrote: I think I couldn't frame the question correctly. Let's say I have a silica surface and I have water droplet on it and after a proper nvt simulation I want to calculate the interaction energy of the water droplet with the surface then how can I

Re: [gmx-users] Question on energygrps setting

I think I couldn't frame the question correctly. Let's say I have a silica surface and I have water droplet on it and after a proper nvt simulation I want to calculate the interaction energy of the water droplet with the surface then how can I use the energy grps option for analysis. Thanks

Re: [gmx-users] Question on energygrps setting

On 5/7/20 10:49 AM, Devargya Chakraborty wrote: Suppose my system contains an anion a cation and water and I have done an nvt simulation.after the completion I want to see the energy profile of the individual groups like the cation or the anion etc. Can anybody guide me how to use the energy

Re: [gmx-users] Question on energygrps setting

Suppose my system contains an anion a cation and water and I have done an nvt simulation.after the completion I want to see the energy profile of the individual groups like the cation or the anion etc. Can anybody guide me how to use the energy grps option in analysing that. Thanks Devargya

Re: [gmx-users] Info regarding restrained minimization, equilibration & production

Thanks Justin. I will then add manually the constraints on the topology file. Paolo Il giorno gio 7 mag 2020 alle ore 14:56 Justin Lemkul ha scritto: > > > On 5/7/20 8:53 AM, Paolo Costa wrote: > > Dear Justin > > > > that means when I generate the topology file by pdb2gmx I will add >

Re: [gmx-users] Info regarding restrained minimization, equilibration & production

Dear Justin that means when I generate the topology file by pdb2gmx I will add manually the section [constraints] on it? Thanks. Paolo Il giorno gio 7 mag 2020 alle ore 14:50 Justin Lemkul ha scritto: > > > On 5/7/20 8:47 AM, Paolo Costa wrote: > > Dear Justin, > > > > I thought too. > > In

Re: [gmx-users] Info regarding restrained minimization, equilibration & production

On 5/7/20 8:53 AM, Paolo Costa wrote: Dear Justin that means when I generate the topology file by pdb2gmx I will add manually the section [constraints] on it? I suggest you look into the manual to understand different ways of applying constraints. You can either convert bonds into

Re: [gmx-users] Info regarding restrained minimization, equilibration & production

On 5/7/20 8:47 AM, Paolo Costa wrote: Dear Justin, I thought too. In case, could you please indicate me how I can constrain the interatomic distance of a desired molecule, in such case the POM molecule? Define [constraints] in the topology for all relevant interatomic distances. -Justin

Re: [gmx-users] Info regarding restrained minimization, equilibration & production

Dear Justin, I thought too. In case, could you please indicate me how I can constrain the interatomic distance of a desired molecule, in such case the POM molecule? Thanks a lot. Paolo Il giorno gio 7 mag 2020 alle ore 14:44 Justin Lemkul ha scritto: > > > On 5/7/20 8:41 AM, Paolo Costa

Re: [gmx-users] Info regarding restrained minimization, equilibration & production

On 5/7/20 8:41 AM, Paolo Costa wrote: Dear Justin, thanks a lot for your valuable information. The system (Keggin anion, POM) I am trying to simulate is almost identical to the one already studied in literature (doi: 10.1021/jp077098p). In the SI of this work, the authors stated "*Keggin

Re: [gmx-users] Info regarding restrained minimization, equilibration & production

Dear Justin, thanks a lot for your valuable information. The system (Keggin anion, POM) I am trying to simulate is almost identical to the one already studied in literature (doi: 10.1021/jp077098p). In the SI of this work, the authors stated "*Keggin anions are treated as rigid particles thus

Re: [gmx-users] Need help creating md.mdp for silica(quartz)?

Hello Justin, so I believe it's just pbc visualization stuff going on then.. okay.. yes you can do it then from trjconv . Regards, Debashish On Thu, 7 May 2020, 14:14 Debashish Banerjee, wrote: > Hello Ekatherina, I did not reach a point in my simulations where I have > used freeze command,

Re: [gmx-users] Info regarding restrained minimization, equilibration & production

On 5/6/20 11:35 AM, Paolo Costa wrote: Dear Gromacs users, I am interested on studying the interaction between large metal cluster anions (polyoxometallates, POM) with different organic cations (e.g perylenes, etc..) in water. I have already the non bonded parameters of POMs from literature,

Re: [gmx-users] Question on energygrps setting

On 5/6/20 6:31 PM, Lei Qian wrote: Dear users, I know interaction energy calculation is carried out via energygrps setting in mdp file. Because free energy-related settings do not include this energygrps setting, so I think this energygrps setting may NOT be related to free energy settings.

Re: [gmx-users] Need help creating md.mdp for silica(quartz)?

On 5/7/20 4:24 AM, Ekatherina O wrote: Hello Dr. Dallas Warren, Thank you for the suggestions. But this does not solve the problem of the movement of atoms of quartz layers (upper and lower) located at the borders of the box. I would like the quartz layers to remain intact during the

Re: [gmx-users] Need help creating md.mdp for silica(quartz)?

Hello Ekatherina, I did not reach a point in my simulations where I have used freeze command, but I think for your case, can't you put a position constraint on your quartz layer. In that case, you just have to create an index file having quartz in the group and then you can put postion restraints

Re: [gmx-users] Lincs warning and Bond length not finite

Many thanks Alex for your reply :) You have pressure scaling and LINCS convergence issues, suggesting that > the starting configuration is far from equilibrium, as well as > potentially other issues. > > How to check if my starting configuration is far from equilibrium ? I checked the Temperature

Re: [gmx-users] Free volume variation during the simulation

Many thanks david for the explanation. In did NVT then NPT equilibiration and then the production run, in the production run .mdp file I have the same parameters as in NVT and NPT.mdp files. Does this mean that my simulation is a NVT simulation or NPT ? Is it possible to do only one of them (NVT

Re: [gmx-users] Need help creating md.mdp for silica(quartz)?

Hello Dr. Dallas Warren, Thank you for the suggestions. But this does not solve the problem of the movement of atoms of quartz layers (upper and lower) located at the borders of the box. I would like the quartz layers to remain intact during the modeling process, i.e. atoms did not move and