Re: [gmx-users] solvent evaporation modeling

Hi Sako I did something similar where I dehydrated a system of water molecules, in my case a crystal but the principles are the same. I have uploaded the script at https://github.com/aslarsen/gromacs_dehydration/blob/master/gromacs_dehydration_MPI_V2.py It was used in this paper

Re: [gmx-users] Walls and center of mass motion

Any ideas? Anders On Fri, Oct 13, 2017 at 3:15 PM, Anders Støttrup Larsen <anders...@gmail.com > wrote: > Hi all > > I have been trying to simulate a system containing two walls and a > slab/vacuum. During the simulation water from the slab diffuses into the > vacuum as

[gmx-users] Walls and center of mass motion

Hi all I have been trying to simulate a system containing two walls and a slab/vacuum. During the simulation water from the slab diffuses into the vacuum as intended. The problem is that this causes the slab to move in the z-direction and eventually crash into one of the walls. The slab has a

Re: [gmx-users] ACPYPE now works with GAFF2

Hi Cool, is there any article or citation for GAFF2? Best wishes Anders On Tue, Jan 17, 2017 at 7:44 PM, Alan wrote: > Now one can do: > > acpype -a gaff2 -i ... > > See 'acpype -h' for more details: > > -a ATOM_TYPE, --atom_type=ATOM_TYPE >

Re: [gmx-users] about potential energy calculation

Do you have the same amount of molecules in each simulation? Anders On Fri, Jan 13, 2017 at 12:19 PM, Albert wrote: > Hi Mark. > > thanks a lot for your comments. > > These two peptides are isomers. > > I want to know which conformations is more favourable than the other