[gmx-users] POSITION RESTRAIN ERROR

[Justin Lemkul]

On 9/25/13 6:05 AM, MUSYOKA THOMMAS wrote:
> Dear Users,
> I am running Protein-Ligand MD simulations. Whenever, i get to do the
> Position restrain run of both my protein and ligand, i get this error;
> Making 1D domain decomposition 4 x 1 x 1
> starting mdrun 'Protein in water'
> 50000 steps,    100.0 ps.
> step 0
> Step 8, time 0.016 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.080448, max 2.357673 (between atoms 2458 and 2457)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>     2458   2457   87.8    0.1141   0.3828      0.1140
>     2459   2458   86.7    0.1431   0.3658      0.1430
>     2461   2459   53.2    0.1340   0.1619      0.1340
>     2460   2459   53.2    0.1341   0.1672      0.1340
> Wrote pdb files with previous and current coordinates
>
> Step 9, time 0.018 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 3.823957, max 98.964455 (between atoms 2458 and 2457)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>     2458   2457   78.0    0.3828  11.3959      0.1140
>     2459   2458  101.2    0.3658  10.0612      0.1430
>     2461   2459   85.5    0.1619   2.9966      0.1340
>     2460   2459  119.1    0.1672   4.7966      0.1340
>     2466   2460  141.3    0.1532   3.1407      0.1340
>     2467   2474  120.0    0.1132   0.6682      0.1120
>     2476   2474   39.0    0.1343   0.1077      0.1340
>     2467   2468  108.0    0.1483   0.7201      0.1470
>     2469   2468   33.9    0.1532   0.1473      0.1530
>     2464   2466  114.5    0.1455   0.5169      0.1390
>     2464   2465   44.6    0.1895   0.2021      0.1870
>     2462   2461  112.9    0.1640   5.8194      0.1400
>     2464   2462   87.1    0.1438   2.1170      0.1390
>     2463   2462   43.8    0.1125   1.2153      0.1090
>
> Step 9, time 0.018 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.650577, max 22.438158 (between atoms 2466 and 2460)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>     2466   2464  114.5    0.1455   0.5169      0.1390
>     2465   2464   44.6    0.1895   0.2021      0.1870
>     2464   2462   87.1    0.1438   2.1170      0.1390
>     2462   2463   43.8    0.1125   1.2153      0.1090
>     2462   2461  112.9    0.1640   5.8194      0.1400
>     2459   2461   85.5    0.1619   2.9966      0.1340
>     2459   2460  119.1    0.1672   4.7966      0.1340
>     2459   2458  101.2    0.3658  10.0612      0.1430
>     2458   2457   78.0    0.3828  11.3959      0.1140
>     2466   2460  141.3    0.1532   3.1407      0.1340
>     2474   2467  120.0    0.1132   0.6680      0.1120
>     2468   2467  108.0    0.1483   0.7200      0.1470
>     2469   2468   33.9    0.1532   0.1473      0.1530
>     2476   2474   39.4    0.1343   0.1089      0.1340
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> Warning: 1-4 interaction between 2457 and 2460 at distance 14.992 which is
> larger than the 1-4 table size 2.400 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
>
> Will be glad to learn how to go about it?
>

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

Without a description of your system, the .mdp file for the crashing run, and a 
full accounting of what you have done to prepare the system (EM, prior 
equilibration, etc) there is little point in speculating beyond saying that 
typically crashes are caused by bad .mdp settings or a flawed topology.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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