[gmx-users] DPPC bilayer

This should give you a good starting point for your own modifications. http://www.gromacs.org/pipermail/gmx-users/2006-September/023639.html http://www.pomeslab.com/files/lipidCombinationRules.pdf --original message -- Hello - I have previously asked about a DPPC bilayer and was very helpfully

[gmx-users] DPPC bilayer

Hello - I have previously asked about a DPPC bilayer and was very helpfully answered by Justin (Many thanks!) who pointed me to the Tieleman page: http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies which was a great help, but unfortunately, the itp files are for ffgmx. I've spent

Re: [gmx-users] DPPC bilayer simulation crash

Hi Michael, are you simulating with a constant area, volume or pressure ensemble? If you are using the configuration you mention as a starting point and simulating it with another forcefield, as Mark pointed out, it's not unexpected to find problems. Moreover, equilibration in lipid simulations..

Re: [gmx-users] DPPC bilayer simulation crash

Michael Skaug wrote: I am trying to perform a simulation of 128 dppc in 3655 spc water. I obtained .pdb and .top files from the Biocomputing website at U.Calgary. I do nothing to alter the structure, which must be minimized as it comes err, not minimized - sampled from the ensemble they were u

[gmx-users] DPPC bilayer simulation crash

I am trying to perform a simulation of 128 dppc in 3655 spc water. I obtained .pdb and .top files from the Biocomputing website at U.Calgary. I do nothing to alter the structure, which must be minimized as it comes from the end of a 1 ns simulation. Processing the input files works fine, but the

[gmx-users] DPPC Bilayer Size

Hi All   I am trying to simulate a GPCR protein belonging to the rhodopsin family with amino acid length of 320 residues. Also, I would be using the pre-hydrated DPPC bilayer, can somebody suggest that for a GPCR protein of roughly 320 aa, how big DPPC bilayer would be appropriate to use