Check for bad contacts and/or reduce the timestep if appropriate

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1

GROMACS version:
GROMACS modification: Yes/No
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Dear all,
How to manage this error?
The message is ’ Check for bad contacts and/or reduce the timestep if appropriate.’

Details of the error message is as follows

Command line:
gmx mdrun -deffnm nvt -v

Reading file nvt.tpr, VERSION 2020.2 (single precision)

1 GPU selected for this run.
Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:

Using 8 OpenMP threads
starting mdrun ‘UNNAMED in water’
50000 steps, 100.0 ps.
step 0
Step 3, time 0.006 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000109, max 0.004851 (between atoms 5216 and 5217)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
5216 5218 31.9 0.1110 0.1107 0.1111
5261 5263 34.8 0.1111 0.1111 0.1111

Step 4, time 0.008 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.618063, max 34.995708 (between atoms 5314 and 5315)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
5314 5315 90.0 0.1325 4.7694 0.1325
Wrote pdb files with previous and current coordinates

Step 5, time 0.01 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 6.382772, max 357.989227 (between atoms 6414 and 6415)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
5216 5217 90.0 0.1111 0.4484 0.1111
5216 5218 90.0 0.1111 0.4132 0.1111
5311 5312 90.0 0.1111 0.2867 0.1111
5311 5313 90.0 0.1111 0.2706 0.1111
5314 5315 90.0 4.7694 6.6699 0.1325
6414 6415 70.5 0.0960 34.4630 0.0960
Wrote pdb files with previous and current coordinates

Step 6, time 0.012 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 42134.101562, max 1686944.500000 (between atoms 5311 and 5312)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
5216 5217 90.0 0.4484 5.9896 0.1111
5216 5218 120.6 0.4132 29.3230 0.1111
5311 5312 90.6 0.2867 187419.6406 0.1111
5311 5313 97.6 0.2706 187419.3594 0.1111
5314 5315 45.3 6.6699 14.6663 0.1325
6395 6423 90.0 0.1111 0.5319 0.1111
6395 6424 90.0 0.1111 0.1256 0.1111
6395 6425 90.0 0.1111 0.1404 0.1111

step 6: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)

2

Your system is unstable and blowing up.

http://manual.gromacs.org/documentation/current/user-guide/terminology.html#blowing-up

3

I tried with Gromacs 2018.1 also. It shows errors as detailed below.
How to overcome this error ?

( ERROR 1 [file lig.itp, line 575]; Duplicate atom index (19) in virtual_sites3)

I tried after deleting the line which returned an error message. but still the problem does not get resolved.

Command line:
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 1
The above command returns following ‘error message’ while using with " ions.mdp "

NOTE 1 [file ions.mdp]:
ERROR 1 [file lig.itp, line 575]:
Duplicate atom index (19) in virtual_sites3

I tried after deleting the line 575, but it produces another error at a later stage
gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr
gmx mdrun -deffnm nvt -v

starting mdrun ‘XX in water’
50000 steps, 100.0 ps.

Step 4, time 0.008 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000442, max 0.021883 (between atoms 5216 and 5218)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
5216 5217 61.7 0.1111 0.1125 0.1111
5216 5218 36.6 0.1111 0.1135 0.1111

4

The section I pointed you to, and the one following it, provide details on what you need to look into to determine what the problem is. Work your way through those points.

As for the new error, what FF and how did you generate the topology files? Sounds like it might be an issue with that, see https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg40797.html

When you get an error, put the text of it into a search engine and see what comes up. Faster for you to get a solution that way. Many times what you are seeing others have come across before and asked for assistance with.