Re: [gmx-users] Membrane protein simulation

Unfortunately genbox will put waters anywhere there is a space, including inside the membrane. This can easily be fixed by making a script to remove waters that are z +/- ~2 nm from the membrane center (you should run g_density on the system to figure out the optimal distance filter). You can

[gmx-users] opls parameters fir gramicidin terminal groups

Does anyone know where I can find opls-aa parameters for strange peptide terminal groups, such as the formyl N-terminus and ethanolamine C-terminus of gramicidin A? I know for charmm you can auto-generate these using swissparam but I don't know of any equivalent for opls. Thanks, --

Re: [gmx-users] MARTINI / all-atom mapping

. Mike On Tue, Aug 30, 2011 at 3:06 AM, XAvier Periole x.peri...@rug.nl wrote: it must be some example of mapping lipids on the website: cgmartini.nl On Aug 30, 2011, at 3:55 AM, Michael Daily wrote: Hi all, I am trying to reverse-map some martini lipids to united atom. In order to do

[gmx-users] MARTINI / all-atom mapping

Hi all, I am trying to reverse-map some martini lipids to united atom. In order to do this, I'd prefer to have an EXACT definition of the aa-to-cg mapping. I cannot find this, only an imprecise graphic, in the MARTINI paper; the martini.itp file doesn't appear to list which heavy atoms are

[gmx-users] surface area calculations for MARTINI

Hi, I'm trying to do some surface area calculations on MARTINI models using APBS, which requires supplying vdw radii via a pqr file. Given how MARTINI treats LJ interactions (0.47 nm radius for all particle types), how do I calculate reasonable effective vdw radii? Obviously the PC headgroup

[gmx-users] Using genbox to REMOVE solvent

Hi all, I am looking for a relatively easy way to make minor modifications to a solvated system in gromacs without having to replace the whole solvent layer. Specifically, I'm swapping out some molecules (technically, just swapping residue and atom names) in a MARTINI model and I think this

Re: [gmx-users] Using genbox to REMOVE solvent

the system can be regenerated from scratch with a new lipid config overnight. On Wed, Aug 17, 2011 at 11:54 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 18/08/2011 4:32 PM, Michael Daily wrote: Hi all, I am looking for a relatively easy way to make minor modifications to a solvated

Re: [gmx-users] Using genbox to REMOVE solvent

And I am happy to report that this method produces a viable starting structure :) On Thu, Aug 18, 2011 at 7:02 PM, Michael Daily mdaily.w...@gmail.comwrote: I tried an experiment similar to yours - after converting the POPE's to POPC's when I remove all waters that are near the (lipid

Re: [gmx-users] oplsaa vs. charmm

Do you have some experimental data to compare to your IDP simulations, like X-ray scattering or some such? I'd imagine that IDP simulations with either forcefield would only be qualitatively accurate given that the forcefields are calibrated, as you say, on rigid

Re: [gmx-users] implicit solvent LINCS errors

The following mdp file produces a successful dynamics run out to 100K steps / 200 ps. What I discovered is this: Using the md integrator, it is necessary to turn off pressure coupling. However, pressure coupling works with sd (Langevin) integrator. Mike --- ; title and include files