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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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