[gmx-users] LINCS warning

Farial Tavakoli faryal.tavakoli at gmail.com
Sun Nov 11 10:01:21 CET 2018

Dear Mark

Thank you for your reply
I got dt=0.00005 ps and run EM and NVT on the ligand in vacuo and got this
EM results:

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
                 (ns/day)    (hour/ns)
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
converting files?
If it is needed I will send you my files to you.

Thanks in advance

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