I am simulating electroporation in varying cholesterol content in the lipid membrane. I am trying to simulate each system exactly in the same conditions and with the same protocols, but the system with 30% of cholesterol in the membrane does not work... I have tried the simulation twice, but everytime it is the same. Interestingly, nothing was wrong with other concentrations such as 10%, 50% and so on....
Before running the simulation, I have equilibrated the system under NPT conditions (100ns). The simulation, which I want to run is 10ns NVT with extended z axis.
The problem is that the simulation starts and it produces .log, .xtc, .edr and .trr files and it stops even before any steps of simulation.
I don't know how to interpret that...
I need a little more information. Are there any errors reported in the log file?
Yes, there is. It says: "1 particles communicated to PME rank 4 are more then 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x."
Yesterday I tried to overcome this problem by changing the Nose-Hoover thermostat into Verlet. Because I am starting my adventure with MD, I am not sure if I can do that...
This is not a problem of an integrator but communication - the atoms of a molecule are to far away from each other. Visualize your system and look for unusual long bonds.
BTW, what do you mean by "10ns NVT with extended z axis"? Did you manually change the box bounds in the z dimension?
You may be right, the system had water molecules in the vacuum.
Yes, I have manually extended the z axis of the system (I have changed the length in the gro file). It's because I wanted to create vacuum above and below my system.
Here's your problem - if any molecule had a bond across the z boundary, it would become elongated beyond the communication cutoff after your change. You have to unwrap the coordinates in that direction. It can be done with software such as VMD.
Also note that by creating the vacuum your system is no longer in equilibrium since you created two new surfaces.
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