[gmx-users] Error during NVT
Justin Lemkul
jalemkul at vt.edu
Sat Jan 31 23:13:53 CET 2015
On 1/31/15 3:35 AM, neha bharti wrote:
> Hello all
>
> I am performing molecular dynamics simulation of Protein-Ligand complex in
> water.
> I docked the ligand molecule and performed its molecular dynamics
> simulation using GROMOS96 53a6 force field. The ligand itp file is
> generated with the help of prodrg.
>
Raw PRODRG topologies are notoriously bad. See
http://pubs.acs.org/doi/abs/10.1021/ci100335w
> But during the NVT the system giving the following error message.
>
>
> Step 0, time 0 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 3.475746, max 40.868980 (between atoms 2137 and 2136)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 2174 2175 71.9 0.1010 0.0941 0.1000
> 2172 2174 74.8 0.1370 0.2308 0.1340
> 2079 2080 59.1 0.1531 0.2078 0.1530
> 2080 2081 87.3 0.1540 0.3014 0.1530
> 2082 2084 107.8 0.1257 1.2267 0.1250
> 2082 2083 52.0 0.1243 0.6202 0.1250
> 2137 2136 88.0 0.1345 5.5686 0.1330
> 2139 2137 123.5 0.1403 5.7269 0.1390
> 2138 2137 90.3 0.1102 4.0876 0.1090
> 2141 2139 88.3 0.1396 2.0444 0.1390
> 2140 2139 83.8 0.1095 0.5954 0.1090
> 2143 2141 90.4 0.1402 3.6931 0.1390
> 2142 2141 89.3 0.1095 1.2808 0.1090
> 2145 2143 89.3 0.1344 4.1272 0.1330
> 2144 2143 90.1 0.1103 2.9604 0.1090
> 2146 2145 99.7 0.1337 0.1015 0.1330
> 2147 2146 88.7 0.1354 0.2207 0.1330
> 2135 2134 67.1 0.1011 0.1855 0.1000
> 2147 2134 77.5 0.1355 0.2555 0.1330
> 2136 2134 117.3 0.1338 0.1883 0.1330
> 2005 2007 87.6 0.1475 2.9044 0.1330
> 1995 1996 138.0 0.1602 1.7197 0.1530
> 1997 1999 135.4 0.1334 0.1773 0.1330
> 1999 2003 45.6 0.1331 0.1962 0.1330
> 1999 2000 41.3 0.1091 0.1553 0.1090
> 1997 1998 126.5 0.1334 0.1666 0.1330
> 1998 2001 41.8 0.1330 0.1821 0.1330
> 1993 1995 128.4 0.1540 1.7394 0.1470
> 1991 1992 127.1 0.1238 0.1164 0.1230
> 1981 1991 71.5 0.1537 0.1183 0.1530
> 2007 2009 63.9 0.1466 4.1114 0.1470
> 2007 2008 64.6 0.0989 2.4912 0.1000
> 2014 2016 79.3 0.1352 0.2778 0.1330
> 2014 2015 53.1 0.1247 0.3961 0.1230
> 2016 2018 65.0 0.1480 0.0770 0.1470
> 2016 2017 108.7 0.1007 0.1168 0.1000
> 2167 2162 87.8 0.1420 3.1317 0.1390
> 2163 2162 84.0 0.1418 1.3696 0.1390
> 2165 2163 82.9 0.1400 1.1678 0.1390
> 2164 2163 84.9 0.1100 0.9701 0.1090
> 2171 2165 64.1 0.1417 0.3248 0.1390
> 2166 2165 79.7 0.1101 0.4717 0.1090
> 2169 2167 87.8 0.1401 4.7298 0.1390
> 2168 2167 88.1 0.1102 2.2550 0.1090
> 2171 2169 88.0 0.1420 3.3899 0.1390
> 2170 2169 86.2 0.1103 1.1563 0.1090
> 2172 2171 50.8 0.1411 0.4534 0.1390
> 2157 2149 33.0 0.1400 0.2001 0.1390
> 2157 2155 38.3 0.1397 0.2003 0.1390
> 2158 2157 66.0 0.1346 0.2301 0.1330
> 2160 2158 68.3 0.1366 0.2874 0.1340
> 2159 2158 73.0 0.1009 0.1552 0.1000
> 2162 2160 68.3 0.1411 0.7325 0.1390
> 2161 2160 73.0 0.1246 0.2199 0.1230
> 2009 2014 125.4 0.1616 2.0048 0.1530
> 2009 2010 123.0 0.1607 1.8944 0.1530
> 2010 2011 71.0 0.1542 0.5384 0.1530
> 2011 2013 114.5 0.1253 0.1983 0.1250
> 2011 2012 106.1 0.1253 0.1982 0.1250
> 2174 2172 67.9 0.1370 0.3000 0.1340
> 2173 2172 73.5 0.1247 0.2299 0.1230
> 2176 2174 61.6 0.1347 0.2307 0.1330
> 2175 2174 75.9 0.1010 0.1757 0.1000
> 2179 2176 41.2 0.1398 0.2094 0.1390
> 2177 2176 39.6 0.1398 0.2097 0.1390
>
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> step 0Warning: 1-4 interaction between 2136 and 2141 at distance 2.463
> 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
> -------------------------------------------------------
> Program mdrun, VERSION 4.5.5
> Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/pme.c, line: 538
>
> Fatal error:
> 1 particles communicated to PME node 4 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension x.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
>
>
> But when I change the lincs constraints from all_bond to h-bonds it run
> successfully. Is this a correct way??
No. The constraints are not the source of the problem, they're just the first
thing to fail when the model physics breaks. You're reducing the number of
bonds that are constrained, but that doesn't eliminate the fact that your
initial model had something physically wrong with it.
Troubleshoot properly with the advice at
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System,
specifically point 2.
-Justin
> Following are my em.mdp and nvt.mdp file :
>
> EM.mdp file:
>
> title = Minimization ; Title of run
>
> ; Parameters describing what to do, when to stop and what to save
> integrator = steep ; Algorithm (steep = steepest descent
> minimization)
> emtol = 1000.0 ; Stop minimization when the maximum force <
> 10.0 kJ/mol
> emstep = 0.01 ; Energy step size
> nsteps = 50000 ; Maximum number of (minimization) steps to
> perform
> energygrps = Protein <0> ; Which energy group(s) to write to disk
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist = 1 ; Frequency to update the neighbor
> list and long range forces
> ns_type = grid ; Method to determine neighbor list
> (simple, grid)
> rlist = 1.0 ; Cut-off for making neighbor list (short
> range forces)
> coulombtype = PME ; Treatment of long range electrostatic
> interactions
> rcoulomb = 1.0 ; long range electrostatic cut-off
> rvdw = 1.0 ; long range Van der Waals cut-off
> pbc = xyz ; Periodic Boundary Conditions
>
>
> NVT.mdp file:
>
> title = Protein-ligand complex NVT equilibration
> define = -DPOSRES ; position restrain the protein and ligand
>
> ; Run parameters
> integrator = md ; leap-frog integrator
> nsteps = 1000000 ; 2 * 1000000 = 2000 ps
> dt = 0.002 ; 2 fs
> ; Output control
> nstxout = 500
> nstvout = 500
> nstenergy = 500
> nstlog = 500
> energygrps = Protein <0>
> ; Bond parameters
> continuation = no
> constraint_algorithm = lincs
> constraints = h-bonds
> lincs_iter = 1
> lincs_order = 4
> ; Neighborsearching
> ns_type = grid ; search neighboring grid cells
> nstlist = 10 ; 20 fs, largely irrelevant with Verlet
> rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)
> rlist = 1.4
> rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
>
> ; Electrostatics
> coulombtype = PME ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order = 4 ; cubic interpolation
> fourierspacing = 0.16 ; grid spacing for FFT
> ; Temperature coupling
> tcoupl = V-rescale ; modified Berendsen thermostat
> tc-grps = Protein_<0> Water_and_ions ; two coupling groups - more
> accurate
> tau_t = 0.1 0.1 ; time constant, in ps
> ref_t = 300 300 ; reference temperature, one
> for each group, in K
> ; Pressure coupling
> pcoupl = no ; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc = xyz ; 3-D PBC
> ; Dispersion correction
> DispCorr = EnerPres ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel = yes ; assign velocities from Maxwell distribution
> gen_temp = 300 ; temperature for Maxwell distribution
> gen_seed = -1 ; generate a random seed
>
>
> Please Help.
>
> With Regards
> Neha Bharti
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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