Dear users,
I am trying to simulate a non protein molecule and have included the
necessary parameters in the ff*.rtp file. I first encountered an error in
the grompp step, so i modified my .mdp files such that the rlist, rvdw and
rcoulomb values are set to 0.5. Now, while carrying out the mdrun for the
position restraint step, I am getting a segmentation fault and a LINCS
warning for the dihedrals that exceed 30. I do not know how to proceed and
I'm using version 3.3.3 so the bug in the earlier version should have been
fixed. I have also tried other suggestions in the forum with no effect. Here
is my pr.mdp file
title = cpeptide position restraining
warnings = 10
cpp = /lib/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 10000 ; total 20.0 ps.
nstcomm = 1
nstxout = 10
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
rlist = 0.5
coulombtype = PME
rcoulomb = 0.5
rvdw = 0.5
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tau_t = 0.1 0.1
tc-grps = Protein other
ref_t = 300 300
; Pressure coupling is not on
Pcoupl = no
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
and this is the error I am encountering.
Back Off! I just backed up md.log to ./#md.log.2#
Reading file NOR_pr.tpr, VERSION 3.3.3 (single precision)
Back Off! I just backed up ener.edr to ./#ener.edr.2#
starting mdrun 'Protein in water'
10000 steps, 20.0 ps.
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 361281.968750 (between atoms 2 and 7) rms 231973.328125
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 89.7 0.1530 43840.2148 0.1530
1 5 89.8 0.1530 44279.3516 0.1530
2 3 89.3 0.1530 51527.6133 0.1530
2 7 89.1 0.1530 55276.2969 0.1530
3 4 89.5 0.1530 22948.2949 0.1530
3 6 88.5 0.1530 20192.1895 0.1530
4 5 88.8 0.1530 8407.1387 0.1530
4 7 89.3 0.1530 26344.8340 0.1530
5 6 91.3 0.1530 33359.8477 0.1530
6 7 88.6 0.1530 13846.0684 0.1530
Segmentation fault
I have been trying to solve this problem for quite some time now. It would
be very helpful if you can suggest some way to work around this problem.
regards
Rukmani Sridharan
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