Hi,
Please keep such discussions on the mailing list so that others can
learn and contribute from the discussion and its archive.
On point, this .mdp file has a feature about which I have already
indicated a link that highlights its undesirability. Moreover, this .mdp
file did not produce the simulation that crashed, because you've
previously reported the same output from a different .mdp file. That
kind of mismatch makes it hard for people to want to help...
The link Justin provided originally has tips on how to diagnose what is
going wrong on systems that are blowing up. You should read that link
and follow links from it. In the absence of new information from you,
there's really nothing else that we can help with.
Mark
-------- Original Message --------
Subject: Check for bad contacts and/or reduce the timestep
Date: Fri, 09 Dec 2011 13:28:41 +0530
From: pragna lakshmi <[email protected]>
To: [email protected]
Dear Mark,
i am trying to do protein-ligand simulation. while
running energy minimization step maximum force is on atom 2099. And it
was completed in 696 steps. I used pr.mdp file for equilibration which
is given below.
title = protein
cpp = /lib/cpp ; location of cpp on SGI
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 50000 ; total 20.0 ps.
nstcomm = 1
nstxout = 250 ; output coordinates every 0.5 ps
nstvout = 1000 ; output velocities every 2.0 ps
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in four groups
Tcoupl = V-rescale
tau_t = 0.1 0.1 0.1 0.1 0.1
tc_grps = protein ZN sol IMP NA+
ref_t = 300 300 300 300 300
; Pressure coupling is on
Pcoupl = no
pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
pr.mdp step run well. But at
final md step it is showing the following error.
Step 105692, time 211.384 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.002880, max 0.071917 (between atoms 2097 and 2095)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2098 2099 38.6 0.1330 0.1371 0.1330
2097 2098 45.2 0.1330 0.1370 0.1330
.
.
.
.
Step 226039, time 452.078 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 42.444550, max 1059.016235 (between atoms 2098 and 2099)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2095 2094 31.6 0.1441 10.5310 0.1250
2113 2114 40.8 0.1471 0.1950 0.1470
2117 2112 36.4 0.1521 0.1902 0.1520
2111 2113 81.7 0.1535 0.2949 0.1520
2111 2112 83.9 0.1534 0.2900 0.1520
2111 2110 113.2 0.1833 0.8261 0.1780
2109 2110 43.8 0.2063 11.5418 0.1750
2107 2109 38.3 0.1516 11.2487 0.1390
2107 2108 103.0 0.1581 11.5450 0.1530
2106 2107 77.4 0.1333 30.0780 0.1530
2104 2105 140.0 0.1080 2.2354 0.1000
2102 2104 34.2 0.1426 16.8737 0.1430
2102 2103 89.9 0.1637 15.4076 0.1530
2101 2106 142.0 0.2077 63.6808 0.1530
2101 2102 132.5 0.1659 62.8960 0.1530
2101 2099 174.7 0.5646 127.3807 0.1390
2099 2100 160.1 0.5219 101.4140 0.1230
2106 2098 166.3 0.2022 76.2729 0.1480
2098 2099 174.8 0.6156 140.9822 0.1330
2097 2109 149.5 0.1057 36.9859 0.1330
2097 2098 159.4 0.2818 84.7773 0.1330
2097 2095 164.8 0.1042 37.0501 0.1330
2095 2096 70.7 0.1482 9.8470 0.1250
Wrote pdb files with previous and current coordinates
There were 4 inconsistent shifts. Check your topology
Warning: 1-4 interaction between 2094 and 2098 at distance 44.117 which
is larger than the 1-4 table size 2.000 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
.
.
.
.
1416 1417 89.7 0.1530 705915256832.0000 0.1530
1414 1416 90.4 0.1470 419510747136.0000 0.1470
1414 1415 92.3 0.1000 45284384768.0000 0.1000
1412 1414 89.5 0.1330 55051784192.0000 0.1330
1412 1413 106.4 0.1230 13457604608.0000 0.1230
1409 1411 119.2 0.1530 519590400.0000 0.1530
1409 1410 107.4 0.1530 519590400.0000 0.1530
1408 1412 99.1 0.1530 14933683200.0000 0.1530
1408 1409 98.3 0.1530 4102264576.0000 0.1530
1406 1408 98.5 0.1470 4076032256.0000 0.1470
1406 1407 107.8 0.1000 606216384.0000 0.1000
1404 1406 122.9 0.1330 606216384.0000 0.1330
1404 1405 31.5 0.1230 0.1567 0.1230
2120 2122 105.2 0.1473 84501076367114240.0000 0.1470
2120 2121 105.8 0.1473 83934295302864896.0000 0.1470
2118 2120 95.0 0.1349 219396825084329984.0000 0.1340
2118 2119 96.0 0.1236 223179042004664320.0000 0.1230
t = 452.080 ps: Water molecule starting at atom 36608 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)
I understood that the force is maximum on atom 2099 and it might be the
reason for this problem. i have gone through this link. But i am really
fail to trouble shoot this error. Could you please help me out in
getting solution for this problem. I have been trying different ways to
solve it out. But nothing went well. I am Sorry for mailing you personally.
--
T.Pragna Lakshmi,
Junior Scientist,
Vision Research Center,
Sankara Netralaya,
Chennai,
India.
Pin: 600006.
--
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