Re: [gmx-users] Gromos DPPC bilayer: different results for 4.0.7 and 4.6.5

Hi, I ran into the same problem comparing the subsequent G54A7 lipid force field for DPPC. We could trace the relevant (trajectory-changing) differences in the code down to the transition Gromacs 4.0.7 - 4.5., and here to the change in the multistep update algorithm. Up to Gromacs 4.0.7, the

[gmx-users] tabulated potentials - cutoff

Hi, I'm using tabulated potentials to create a hole in a membrane. I define three groups: 2 dummy-atoms, all hydrophobic lipid chains, and rest. For the interactions between the dummy atoms and the hydrophobic chains I define an exclusively repulsive potential. All other interactions are

Re: [gmx-users] tabulated potentials - cutoff

So that means the electrostatics are calculated as given in the tables and no long range electrostatics corrections (like PME or RF) are applied? Cheers Sabine Am 28.04.2014 18:28, schrieb Justin Lemkul: On 4/28/14, 9:19 AM, Sabine Reisser wrote: Hi, I'm using tabulated potentials

Re: [gmx-users] tabulated potentials - cutoff

model was working correctly anyway, right? ;-) Mark On Mon, May 5, 2014 at 1:25 PM, Sabine Reisser sabine.reis...@kit.eduwrote: But I cannot have specific interactions between two groups and normal PME for the rest, right? Cheers Sabine Am 05.05.2014 10:41, schrieb Mark Abraham: On May

Re: [gmx-users] mdrun -nsteps

usable unless you know for sure what is in your checkpoint. The current meaning for -nsteps means that it is easy to write a job submission script e.g. for 2 hours doing 50,000 more steps - which is awkward otherwise. Cheers, Mark On Tue, Feb 17, 2015 at 12:10 PM, Sabine Reisser sabine.reis

[gmx-users] Flat bottom position restraints

Hi, I want to use inverse FB pos res to construct a layer in the xy plane where my peptides are not allowed to go, to facilitate binding to the upper leaflet of my membrane instead of to the lower leaflet of the neighboring periodic image. In the manual it says I need three parameters g r

[gmx-users] mdrun -nsteps

Hi, just to be sure: is it intended, that the -nsteps option in mdrun (which is a great feature in general!) actually appends the given number of steps rather than overriding the mdp option? This is what I do: - grompp with mdp file with 5000 steps - mdrun - mdrun -nsteps 1 steps The

Re: [gmx-users] Flat bottom position restraints

Here's the pdf. Am 13.02.2015 14:03, schrieb Sabine Reisser: Ok, I figured it out. With inverse FB pos res, the atoms are pushed away from there initial positions. Compare attached pdf, which shows the z coordinate of the first atom of 3 peptides, with and without the position restraints

Re: [gmx-users] Flat bottom position restraints

the atoms/peptides are pushed, this doesn't help in my case. Cheers Sabine Am 13.02.2015 12:14, schrieb Sabine Reisser: Hi, I want to use inverse FB pos res to construct a layer in the xy plane where my peptides are not allowed to go, to facilitate binding to the upper leaflet of my membrane

Re: [gmx-users] find out tpx version of tpr

ts it to the log file, or likely gmx dump and gmx check also do so. Mark On Mon, 23 May 2016 11:12 Sabine Reisser <sabine.reis...@kit.edu> wrote: Hello, how can I find out the tpx version of a tpr file? Cheers Sabine -- Gromacs Users mailing list * Please search the archive at http:/