[gmx-users] LINCS warning

[Mark Abraham]

Hi,

I can't tell whether that's a periodicity artefact in your visualization,
or the topology is indeed junk. You will likely need to inspect the output
of the tool that generated it. Rarely do these things "just work."

Mark

On Sun, Nov 11, 2018 at 3:01 AM Farial Tavakoli <faryal.tavakoli at gmail.com>
wrote:

> 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
> results:
> 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
> Farial
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