[gmx-users] LINCS warning
faryal.tavakoli at gmail.com
Sun Nov 11 10:01:21 CET 2018
Thank you for your reply
I got dt=0.00005 ps and run EM and NVT on the ligand in vacuo and got this
Steepest Descents converged to machine precision in 80 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = -3.4145945e+03
Maximum force = 6.6494578e+04 on atom 81
Norm of force = 1.0602226e+04
and NVT results:
starting mdrun 'mig'
200000 steps, 10.0 ps.
step 199900, remaining wall clock time: 0 s
Writing final coordinates.
step 200000, remaining wall clock time: 0 s
Core t (s) Wall t (s) (%)
Time: 349.726 87.431 400.0
Performance: 9.882 2.429
I checked ligand.gro (generated using acpype script) and nvt.gro (generated
by dt = 0.00005) files by VMD and noticed the phosphate groups were not
bound to tyrosine residues in ligand.gro and there was bad contacts in them
in nvt.gro . Is it because of VMD software or there is a problem in
If it is needed I will send you my files to you.
Thanks in advance
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