[gmx-users] Error during NVT
neha bharti
nehabharty123 at gmail.com
Sat Jan 31 09:35:24 CET 2015
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.
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??
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
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