you may want to have a look at the cutoff used by the force field you
defined your
molecule in! 0.5 is definitely too small.
did you minimized?
if your starting configuration does not correspond to the topology,
the use of position
restrains (-DPOSRES) if you actually define them will be a problem ...
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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