[gmx-users] nvt wouldn't run even after fixing the pdb file

[Dallas Warren]

Have you looked at/visualised the atoms which are causing the problem?
Is there something about the structure in that region?
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 11 December 2017 at 05:02, MD <refmac5 at gmail.com> wrote:
> Hi Gromacs folks,
>
> I was having problems running nvt which gave complaints about non-stable
> system. I have tried minimizing structure at the first place, fixing broken
> residues, using an alternate structure from pdb (same sequence, ) to start
> with but I kept getting the either the same errors as following or
> complaining about non settled water. I have googled and a lot of other
> users solved the problem by minimizing the initial energy and fixing the
> initial structure of pdb files but I have done both and it still wouldn't
> work. I copied the messages after the mdrun nvt as following. Any help
> would be appreciated.
>
> Thanks,
>
> Ming
>
> gmx mdrun -deffnm nvt
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.007935, max 0.215270 (between atoms 4621 and 4623)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.006332, max 0.171341 (between atoms 4621 and 4623)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    4621   4623   30.8    0.1738   0.1675      0.1430
> starting mdrun 'PROTEIN KINASE C in water'
> 50000 steps,    100.0 ps.
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.014407, max 0.495572 (between atoms 4628 and 4630)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    4597   4599   39.4    0.1511   0.1596      0.1345
>    4599   4600   32.7    0.1033   0.1027      0.0997
>    4628   4630   34.6    0.1686   0.2139      0.1430
>    4630   4631   34.8    0.1125   0.1189      0.1080
>    4630   4632   35.9    0.1622   0.1875      0.1538
>    4630   4643   60.7    0.1648   0.2089      0.1490
>    4643   4644   48.5    0.1263   0.1176      0.1230
>    4643   4645   67.1    0.1421   0.1584      0.1300
>
> Step 1, time 0.002 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.009036, max 0.242983 (between atoms 4619 and 4621)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    4619   4620   32.6    0.1180   0.1435      0.1230
>    4623   4626   33.2    0.1741   0.1794      0.1490
>    4626   4627   36.2    0.1159   0.1417      0.1230
>    4630   4631   59.2    0.1189   0.1326      0.1080
>
> Step 2, time 0.004 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.005815, max 0.136241 (between atoms 4630 and 4631)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    4628   4629   31.9    0.1022   0.1010      0.0997
>    4630   4631   88.9    0.1326   0.1227      0.1080
>    4630   4643   32.0    0.1627   0.1588      0.1490
>    4643   4644   33.0    0.1269   0.1354      0.1230
>    4643   4645   35.7    0.1405   0.1469      0.1300
>
> Step 3, time 0.006 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.515541, max 37.148800 (between atoms 4630 and 4631)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    4628   4629   84.6    0.1010   0.0676      0.0997
>    4628   4630   76.9    0.1545   0.0962      0.1430
>    4630   4631   89.7    0.1227   4.1201      0.1080
>    4630   4643   38.3    0.1588   0.3132      0.1490
> ......
> Wrote pdb files with previous and current coordinates
>
> WARNING: Listed nonbonded interaction between particles 4626 and 4631
> at distance 4.033 which is larger than the table limit 2.431 nm.
>
> This is likely either a 1,4 interaction, or a listed interaction inside
> a smaller molecule you are decoupling during a free energy calculation.
> Since interactions at distances beyond the table cannot be computed,
> they are skipped until they are inside the table limit again. You will
> only see this message once, even if it occurs for several interactions.
>
> IMPORTANT: This should not happen in a stable simulation, so there is
> probably something wrong with your system. Only change the table-extension
> distance in the mdp file if you are really sure that is the reason.
>
>
>
> Step 4, time 0.008 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 5215.553278, max 375898.343750 (between atoms 4649 and 4650)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>     199    200   37.9    0.1111   0.1110      0.1111
>    4599   4600   36.0    0.0951   0.1413      0.0997
>    4599   4601   30.4    0.1522   0.1079      0.1430
>    4619   4620   34.1    0.1265   0.1685      0.1230
>    4619   4621   39.3    0.1402   0.0512      0.1345
>    4621   4622   54.5    0.1001   0.0990      0.0997
>  ......
> Wrote pdb files with previous and current coordinates
> Segmentation fault (core dumped)
> --
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