[gmx-users] Fwd: solvent evaporation modeling

Dear André, Thank you for your response. Could you send me such a script? Best -- *** Sako On Mon, Dec 2, 2019 at 12:54 AM SAKO MIRZAIE wrote: > Dear André, > > Thank you for your response. > Could you send me such a script? > > On Sun, Dec 1, 2019

Re: [gmx-users] solvent evaporation modeling

Dear André, Thank you for your response. Could you send me such a script? On Sun, Dec 1, 2019 at 7:15 PM André Farias de Moura wrote: > Dear Sako, > > we did something like that a few years ago, please take a look at DOI > 10.1039/C4CP03519D > for details. > > in a nutshell: you need a script

Re: [gmx-users] solvent evaporation modeling

Dear Sako, we did something like that a few years ago, please take a look at DOI 10.1039/C4CP03519D for details. in a nutshell: you need a script that runs a sequence of short equilibration and production runs after a number of solvent molecules are removed (implying that topology needs to be

[gmx-users] solvent evaporation modeling

Hi All, I want to simulate a polymer: protein system in a way that water solvent will evaporated gradually. How should I do that? What parameters are needed to be included in the mdp file. Best -- *** Sako -- Gromacs Users mailing list * Please

Re: [gmx-users] Charmm27 and Charmm36 atomtypes assignments for polymer

Dear Justin, Thank you very much for your response. I copied the ITP file that generated Charmm-gui. I am sorry for copied this long residue topology. The residue contains two capping groups that belong to first six atoms and the last six atoms. I thought that if I cut the first 6 atoms, the rest

Re: [gmx-users] the a.u. unit in the RMS distribution graph

Thank you Justin, that saved me a lot of time. Best, Lalehan On Sun, Dec 1, 2019 at 3:45 PM Justin Lemkul wrote: > > > On 12/1/19 3:48 AM, Lalehan Ozalp wrote: > > Hello Christian, thank you for providing the patch. However I wonder if > > there is an easier way to convert a.u to frequency -

Re: [gmx-users] Coulomb and vdW energies

On 12/1/19 5:28 AM, Shreyas Kaptan wrote: Hi. I would not say that it is completely unrealistic/unphysical. Especially, the Electrostatic part. If within two subgroups, you could show that there is systematic repulsive or attractive potential, that could lead to some hypothesis about how

Re: [gmx-users] the a.u. unit in the RMS distribution graph

On 12/1/19 3:48 AM, Lalehan Ozalp wrote: Hello Christian, thank you for providing the patch. However I wonder if there is an easier way to convert a.u to frequency - as I need to install GROMACS from the start to install the patch. One more thing, I used version 5.0, not 2019, and the patch

Re: [gmx-users] Coulomb and vdW energies

Hi. I would not say that it is completely unrealistic/unphysical. Especially, the Electrostatic part. If within two subgroups, you could show that there is systematic repulsive or attractive potential, that could lead to some hypothesis about how they interact (e.g. pushing/pulling). Of course,

Re: [gmx-users] the a.u. unit in the RMS distribution graph

Hello Christian, thank you for providing the patch. However I wonder if there is an easier way to convert a.u to frequency - as I need to install GROMACS from the start to install the patch. One more thing, I used version 5.0, not 2019, and the patch is written for the version 2019. Thank you