Hello gmx users, I am working with gmx version 3.3.1 and i am using the ffG43A2x force field. I am currently running 4 simulations : - In 2 simulations the system is a POPE bilayer in water (454 pope with 15800 spc water molecules) - In the 2 other simulations a protein is embedded in the bilayer (something like 1 protein, 360 POPE, 42000 spc water molecules....)
The method of simulation for the 4 systems is as follow : 1)careful minimization of the system energy 2)5 ns NPT with Berendsen weak coupling (1.0 bar, 310 K) The pressure coupling is semi-isotropic. 3)NPT with Nose-Hoover and Parrinello-Rahman couplings (1.0 bar, 310 K) The pressure coupling is still semi-isotropic. I have attached the ".mdp" file of the bilayer simulations. I use quite the same one in the protein simulation (only temperature coupling groups are different). The bilayer simulations are now running for ~35 ns and the protein simulations for 58 ns with N-H and P-R couplings. The mean values of pressure and temperature correspond to the ones expected. But i have problem with the lengths of the box sides : - After 15 ns of simulations (that is to say between 15 and 35 ns for the POPE simulations and 15 to 58 ns for the protein simulations with N-H and P-R couplings) if you consider a small part of the trajectories (5 to 10 ns in length) the values of the box sides (Box-X, Box-Y and Box-Z) seem to have converged to more or less constant values. But, if you look to the whole periode, (15 ns to 35 ns or 15 ns to 58 ns) you realize that Box-X and Box-Y are slightly decreasing in a continuous way while Box-Z is increasing. (The values of Box-X and Box-Y are around 10 nm and the decrease is of 0.1 nm to 0.2 nm depending on the system) This results in a slow but constant decrease in the area per lipid just like the one which can be observed in the paper : Biophysical Journal march 2004 vol. 86 p 1601-1609 on figure 2. I have to say that the 454 pope bilayer has been simulated for several nanoseconds with isotropic Berendsen weak coupling before its use in this project. Of course, in this case, the area per lipid was almost constant. This decrease looks like a real tendancy and i have been simulating my systems for quite a little time : So, - do i have to wait a little more for the area per lipid to tend to converge ? I am afraid it won't happen before a very long time. - do i have to change something in the method ? : is these slight decreases of Box-X and Box-Y and increase of Box-Z something frequent with semi-isotropic P-R weak pressure-coupling ? - Is his problem coming from the lipid parameters ? I have red several papers looking at this point. I want to thank you for the time you take dealing with my problem and i would really appreciate your advises. J-Paul.
pope_mdout.mdp
Description: Binary data
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