[gmx-users] Question about water insertion

I have one water molecule in my gro file as below: TIP4P 4 1SOL OW1 0.054 0.005 0.022 1SOLHW12 0.009 0.072 0.073 1SOLHW23 0.142 0.041 0.008 1SOL MW4 0.060 0.018 0.026 0.00 0.000 0.000

[gmx-users] gmx solvate problem

Hi All, I’m simulating a box of tip4p ice. when I use the gmx solvate to fill the top and below part of the ice surface with solvent (the solvent is tip4p water), some of water molecules go to inside of the ice layers. I did not receive any errors, but the coordinate files became messy after

Re: [gmx-users] selecting atoms in index file

in my > index file, should I delete these atoms from surfaces groups. let me > explain better. Now I have 2 groups in my index file Sol and > Kaoli(surface). I should select some atoms from the Kaoli. So first I > define the atoms that I want to select in a seperate group, then I should > e

[gmx-users] selecting atoms in index file

Dear All, I want to create an index file and select some especial atoms in a surface. My problem is that I have only one residue for the whole surface. How can I select the atoms on the surface as a different groups in my index file? Thank you in advance, Golnaz -- Gromacs Users mailing list *

[gmx-users] clayff forcefield

Dear usres, I try to write clayff forcefield, and I want to simulate Kaolinite. I have some questions about it. 1) should I write clayff forcefield separately or modify one of the forcefields in share/top? 2) The directory for clayff forcefield should be included ffbonded.itp, ffnonbonded.itp,

[gmx-users] Could not find clayff forcefield

Dear users, I try to implement Clayff forcefield for Kaolinite. I created my force field (I'm not sure about it), but gromacs couldn't find my force field in the directory. Here is my forcefield. ffnonbonded [ atomtypes ] ; name mass chargeptype sigma eps HW 1

[gmx-users] Clayff forcefield

I try to implement CLYFF in gromacs. I created ffbonded.itp, ffnonbonded.itp, atomtype.atp, forcefield.doc, forcefield.itp and molecule.rtp. I want to simulate Kaolinite, and I try to use pdb2gmx to create a topology. My first question is that should I create any other files?

Re: [gmx-users] TIP4P/ice pdb file

list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > >1. TIP4P/ice pdb file (G R) >

[gmx-users] TIP4P/ice pdb file

Dear All, I would like to simulate water using TIP4P/ice potential. My question is that how can I generate .gro file for this simulation? I will use TIP4P/ice topology that is available in SklogWiki, but I cannot understand how can I generate .gro file for this topology. Can I easily use

[gmx-users] Simulation of pure water

Dear all, I want to calculate the relaxation of pure water cell at room temperature and at freezing point, monitoring its equilibration in volume and in potential energy. I have 3 question: 1) Can I use packmol for my initial configuration? if there is any other option,please tell me. 2) Can I

[gmx-users] Simulation of pure water

Dear all, I want to calculate the relaxation of pure water cell at room temperature and at freezing point, monitoring its equilibration in volume and in potential energy. I have 3 question: 1) Can I use packmol for my initial configuration? if there is any other option,please tell me. 2) Can I