[gmx-users] Nose-Hoover + acc-grps

Hello, I'm trying to run non-equilibrium simulations in the NVT ensemble with the "acc-grps" command and the Nose-Hoover thermostat, but I know that there are ways in which an external acceleration can be incompatible with Nose-Hoover. Are these two compatible in the Gromacs code? Thank you,

Re: [gmx-users] Nonequilibrium simulations

I just reread my e-mail and realized that it was posed as a statement and not a question. What I meant was: When I run non-equilibrium simulations in the Gromacs code using "acc-groups", is the additional acceleration considered to contribute to the temperature when velocities are adjusted or

[gmx-users] Nonequilibrium simulations

Hello, I am running non-equilibrium simulations using the "acc-groups" command and the Nose-Hoover thermostat. I just wanted to confirm that in Gromacs code this additional acceleration is not considered to contribute to the temperature when velocities are adjusted. Thank you! Jon -- Gromacs

[gmx-users] g_hbond

Hello, I'm trying to use g_hbond to calculate H-bonds between two different species, but it seems to be counting the donor atom as an acceptor as well. e.g. instead of measuring the H-bonds of water to acetate oxygens, it seems to be measuring the H-bonds of water to acetate oxygens and water

[gmx-users] freezegrps changing coordinates in NPT simulations

Hello again, I'm running a simulation with graphene as a periodic molecule. I've frozen the carbons in place in the mdp file using: freezegrps = CG_CE freezedim= Y Y Y but when I run an NPT simulation, the entire system shrinks (including moving the carbons

[gmx-users] PBC no domain decomposition error

Never mind my previous message. When I included periodicmolecule = yes in the mdp file, I believe that took care of the problem. Thanks, Jon - Hey! I ran into an issue when simulating graphene sheets with periodic boundary conditions. It said:

Re: [gmx-users] n2t file format for similar atoms

Okay, that sounds good. Thank you! Jon On 5/6/15 1:22 PM, jwill...@andrew.cmu.edu wrote: Hello, I'm trying to specify two different hydroxyl hydrogen atoms in the n2t format: Hopls_9880.435 1.0079 1O 0.0945 and Hopls_1170.4238 1.008 1 O 0.1 for a

[gmx-users] n2t file format for similar atoms

Hello, I'm trying to specify two different hydroxyl hydrogen atoms in the n2t format: Hopls_9880.435 1.0079 1O 0.0945 and Hopls_1170.4238 1.008 1 O 0.1 for a hydroxyl group on graphene and water, respectively. When performing x2top, it seems to assume all Hs in the

[gmx-users] pdb2gmx

Hello, I was under the impression that pdb2gmx was supposed to referance the force fields as defined in oplsaa.ff/forcefield.itp, but it doesn't seem to be for me. To double check, I removed all force field parameters from forcefield.itp and pdb2gmx still ran and got the same result as before.