[gmx-users] About Warnings and Note in Production MD

[Mark Abraham]

On Sun, May 19, 2013 at 1:14 PM, vidhya sankar <scvsankar_agr at yahoo.com>wrote:

> Dear Justin Thank you for previous reply.
>
> I am doing Carbon nano tubes Wrapped by Cyclic peptide
>

That's pretty complex. Can you set up simpler subsets and run them
successfully?


> After NPT and NVT equilibration When i Run Production MD I have got The
> following Notes in terminal
>
>
> NOTE 1 [file CNTCYCfull.mdp]:
>   nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
>   nstcomm to nstcalcenergy
> NOTE 2 [file CNTCYCfull.mdp]:
>   You are using a cut-off for VdW interactions with NVE, for good energy
>   conservation use vdwtype = Shift (possibly with DispCorr)
> NOTE 3 [file CNTCYCfull.mdp]:
>   You are using a cut-off for electrostatics with NVE, for good energy
>   conservation use coulombtype = PME-Switch or Reaction-Field-zero
> NOTE 4 [file gfggZ.top, line 60]:
>   For energy conservation with LINCS, lincs_iter should be 2 or larger.
>

It looks like someone has randomly invented an .mdp from the 1990s :-) Try
to replicate the settings of a model physics that has been published.

if I ignore the Notes  I am Not Able to run .


Notes do not stop you running. They are informational, but maybe you know
enough to proceed without taking direct action. That's your call. Warnings
are for more serious issues, and you have to take direct action to continue
to run in their presence. Errors are fatal, you have to fix them.


> S I have Changed All options Accordingly in .mdp files Then
> When I run I have got the following errors after few Minutes
>
> rms 37613.979597, max 954780.695847 (between atoms 1189 and 1190)
>    1157   1156   34.0    0.0997   0.1118      0.1000
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    1171   1158   36.4    0.1542   0.1972      0.1530
>    1159   1158   34.8    0.1534   0.2022      0.1530
>    1178   1176   67.6    0.1528   2.4354      0.1530
>    1179   1177   79.1    0.1533   0.2981      0.1530
>    1046   1044   35.1    0.1489   0.3847      0.1470
> step 141: Water molecule starting at atom 106721 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> Segmentation fault
>
>
> So I Have reduced the Time step Again I have received the same error as
> follows but this time
>
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> Segmentation fault
>
>
> How to Avoid Should I Equilibrate for Longer  time?  . I Have done 2ns
> Equilibration Only
> Is My equilibration is not enough?
>

Your system is http://www.gromacs.org/Documentation/Terminology/Blowing_Up,
probably because your starting configuration has something unsuitable for
your model physics. Given that you seem to be inventing the latter as you
go, this is not terribly surprising.

Mark


> Thanks In Advance
> --
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