Re: [gmx-users] Replacing a molecule with multiple ions

Hi, Seems like a straightforward task for the scripting language of your choice - even grep and sed can do a decent job. Get rid of all but two of the DMA atoms, change them to whatever ions suit you, and make matching changes to your [molecules] section manually. You may need to reorder to have

[gmx-users] Constant pH simulations

Hi everyone, I was wondering if anyone has any experience or knows of a tutorial site that I could look at for performing constant pH simulations. I've checked out the info on the gromacs.org web site and a few others such as (http://www.mpibpc.mpg.de/247796/usage) but I was wondering if there is

Re: [gmx-users] Constant pH simulations

Hi, Not yet, but we are working on it. Best, Thomas. -- R. Thomas Ullmann, PhD Theoretical Computational Biophysics Max Planck Institute for Biophysical Chemistry Am

[gmx-users] GROMPP COMMAND

Dear GROMACS Users: I have a question regarding using the GROMPP command.. I first used the g_x2top command to convert the *.gro file of a graphene sheet to the *.top file of the graphene sheet by using the forcefield.itp file in the OPLSAA file folder as the following: g_x2top -f graphene.gro

Re: [gmx-users] GROMPP COMMAND

Can you tell how you make your topology file for graphene sheet? Because normal way is to do that, first copy the oplsaa.ff file in your working directory, the make the necessary changes in ffnonbonded.itp file and atomname2type.n2t files. Then run g_x2top. The should not give any error. Thanks

[gmx-users] Implementations of/similar to accelerated MD (aMD) in GROMACS

Hi all, I am interested in using accelerated MD or another method which allows me to sample rare events without specifying collective variables beforehand. The only solution that I have found for GROMACS so far is conformational flooding, but I can't find a reference for its implementation in any