[gmx-users] problem with NVT equilibration for membrane protein
floriane.montanari at univie.ac.at
Mon May 12 11:33:08 CEST 2014
I am working with an homology model of a protein inserted in a POPC membrane.
I first ran minimization on the system, which ended up with I think
"reasonable" values for Fmax and Epot:
Steepest Descents converged to Fmax < 1000 in 1390 steps
Potential Energy = -1.2822042e+06
Maximum force = 8.4696790e+02 on atom 7447
Norm of force = 2.2902491e+01
I am using the Amber99sb forcefield modified to include Berger parameters
for my lipids.
I am now trying to run NVT using the parameter file sent as attachment. I
tried to lower the temperature ref_t / different values of cutoffs
rcoulomb, etc. / a Fourier transform of 0.12 as seen in literature
but all this only ended up in the same error:
Depending on how many threads I launch mdrun with, I get
- either a particles error
3 particles communicated to PME node 3 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
(more or less particles / more or less nodes depending on the runs)
- or a segmentation fault
In any cases, those errors occur right at the end of step 0.
Is there anything I am doing wrong? Can someone give me advices on how to
I can send many other files if needed (my topol file, my minimized system,
I am running gromacs 4.5.3.
Thank you in advance for any help,
More information about the gromacs.org_gmx-users