[gmx-users] נושא: RE: Discontinuity in first time-step velocities for diatomic molecule locally coupled to thermal drain

tcoupl =v-rescale  See grompp .mdp  below  Inon Sharony ינון שרוני "Berk Hess [via GROMACS]" כתב: Hi, You can't have ret_t=0 with Nose-Hoover. We should add a check for this. Cheers, Berk > Date: Thu, 28 Jun 2012 11:15:15 +0300 > From: [hidden email] > To: [hidden email] > Subject:

[gmx-users] refcoord_scaling

I always use refcoord_scaling = com because of the warning that refcoord_scaling = no gives problems: quoting http://manual.gromacs.org/online/mdp_opt.html#pc : "Note that with this option the virial and pressure will depend on the absolute positions of the reference coordinates." I don't see

Re: [gmx-users] refcoord_scaling

On 7/10/12 5:48 PM, Katie Maerzke wrote: Hi all - I'm new to Gromacs (and MD). I can't figure out whether or not refcoord_scaling is important for an NpT simulation. In an MC simulation, when the volume changes, the coordinates of the molecules are also scaled. Does refcoord_scaling control

[gmx-users] refcoord_scaling

Hi all - I'm new to Gromacs (and MD). I can't figure out whether or not refcoord_scaling is important for an NpT simulation. In an MC simulation, when the volume changes, the coordinates of the molecules are also scaled. Does refcoord_scaling control how to handle scaling the molecular coord

RE: [gmx-users] Nose-Hoover does not couple

Hi, This is the same issue as in your other mail: ref_t should be > 0. Cheers, Berk > Date: Tue, 3 Jul 2012 17:38:37 +0300 > From: inons...@tau.ac.il > To: gmx-users@gromacs.org > Subject: [gmx-users] Nose-Hoover does not couple > > I'm performing a ver

RE: [gmx-users] Discontinuity in first time-step velocities for diatomic molecule locally coupled to thermal drain

Hi, You can't have ret_t=0 with Nose-Hoover. We should add a check for this. Cheers, Berk > Date: Thu, 28 Jun 2012 11:15:15 +0300 > From: inons...@tau.ac.il > To: gmx-users@gromacs.org > Subject: [gmx-users] Discontinuity in first time-step velocities for diatomic > molecule locally coupled

Re: [gmx-users] POPC in water

On 7/10/12 6:09 AM, Shima Arasteh wrote: Dear gmx users, I want to simulate a protein in bilayer. The chosen bilayer is POPC. According to Justin's tutorial about KALP15 in DPPC, I would simulate the protein in lipid bilayer and water. In this tutorial I didn't find the simulation of bilayer

[gmx-users] POPC in water

Dear gmx users,   I want to simulate a protein in bilayer. The chosen bilayer is POPC. According to Justin's tutorial about KALP15 in DPPC, I would simulate the protein in lipid bilayer and water. In this tutorial I didn't find the simulation of bilayer in water seperately and it is just going

[gmx-users] Re: bilayers move apart by nanometers upon implementing dihedral restraints on lipid tails

Apparently the restraints that were being used earlier were too strong. I tried weaker restraints, and that worked, with the bilayers not moving apart too quickly. Chris Neale: I did not try BD yet, but that seems to be a good idea. thank you all for the help Himanshu -- View this message in co