Setting up a membrane simulation

From: Pellegrini Eric (
Date: Fri Sep 16 2011 - 02:52:05 CDT

Hi all, I use NAMD 2.8 to simulate a pure DMPC membrane (72 lipids and no protein embedded) surrounded by water molecules. Up to now the trials I did failed with errors such as:     ERROR: Constraint failure in RATTLE algorithm for atom 13561 Looking around on the lists I found some hints but I also got frightened with all the possibilities/parameters that can be tuned (e.g. PMEGridSizeX,Y,Z vs PMEGridSpacing, NPT/NVT vs NPGT, Berendsen vs Nose-Hoover, use or not SurfaceTensionTarget, useConstantRatio, useConstantArea ...), wondering finally if a single bad choice could mess up my simulation. I tried two simulation protocols:     1) Minimization: 10000 steps     2) 100-ps NVT simulation with lipid head groups and water fixed in order that the lipid tail can reorganize     3) 100-ps NVT simulation with whole lipid fixed in order that water can reorganize     4) Equilibration: 1 ns NPT (Langevin piston barostat)     4) Production: 100 ns NPT (Langevin piston barostat) and     1) Minimization: 10000 steps     2) Heating:  NPT (Langevin piston barostat) from 0K to 300K by 100ps-steps of 10K     3) Equilibration: 10 ns NPT (Langevin piston barostat)     4) Production: 100 ns NPT (Langevin piston barostat) which one looks the more reasonable (if there is one ...)? I would also have a few additional questions:     - I read in the NAMD membrane tutorial that in the early steps of the protocol, one should introduce a step where only the tail of the lipid can move       Is that something very important to consider, especially in my case where there is no protein ?     - some people use NPGT via the SurfaceTensionTarget option. Is a standard NPT simulation really so bad for this kind       of simulations ? If I have to consider this option, how to set the value ? Is there some kind of standard one (e.g. 60) ?     - my first protocol starts NVT pre-equilibration with an equilibration in NPT. Now, tt seems to me that NPT simulation would be better in the       sense that my system would always breathe adapting its volume to its need. What do you think ?     - should I prefer the PMEGridX,Y,Z options to PMEGridSpacing (e.g 1.0) ? Sorry in advance for the long and perhaps naive email but with 3-weeks per simulations, testing by myself all these parameters would take quite a while !!! thank you very much Eric

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