Hi Everyone,
I got a serious problem while doing nvt run of a plasma membrane in water. NVT run shows the following error:
Fatal error:
3 particles communicated to PME rank 1 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y.
This usually means that your system is not well equilibrated.
Few pdbs are generated. When I open these pdbs the system has been broken. The number of atoms is reduced from 76000 to 4000. Could anyone please help me out of this problem? Thanks in advance.
I am attaching the screenshots of the initial and final structures of the system.
Hi Wei Rao
The box dimension of my system is 8.26050 X 8.77300 X 12.30 nm3 with the total number of atoms 76794. The electrostatic and van de Waals cut offs are both 1.2 nm. The trajectory file is not generated. Only few pdbs are generated. The system is broken from the first pdb file which is generated during nvt equilibration. Could you comment on that?
I think there should be something wrong with your topology files. Check them carefully to make sure all the atoms in your structure file are compatible with the description in topology file, including .top and .itp. Also make sure the indices of atoms are correct in position restraints.
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