On 1/1/13 8:56 AM, Shima Arasteh wrote:

I have a system of Peptide-popc-ions-water to simulate. I'm trying to run MD 
simulation following the Justin's tutorial of kalp15-DPPC.

The force field which I use, is charmm36.

In NVT step, I get LINCS-warning as follow:
Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 2.460224, max 54.696251 (between atoms 4719 and 4716)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.182707, max 15.613569 (between atoms 4725 and 4726)

When I checked the warning, I see the first warning is related to 2 atoms of 
71POPC, the chain of 71POPC residue is broken near these two atoms. And the 
other warning is related to a bond between H and C in the other POPC residue.

Some settings of nvt.mdp is as:
ns_type        = grid
nstlist        = 5
rlist        = 1.2
rlistlong       = 1.4
rcoulomb    = 1.2
rvdw        = 1.2
pbc        = xyz
vdwtype         = switch
rvdw_switch     = 0.8
; Parameters for treating bonded interactions
continuation    = no
constraint_algorithm = LINCS
constraints    = all-bonds
lincs_iter    = 1
lincs_order    = 4

Do I need to increase the rlistlong? I have done a simulation of POPC-water 
before with these settings, but everything was ok. So what's the problem? 
Anybody may help me?

Don't haphazardly mess with cutoffs.  Doing so usually makes your problem worse.

Think about it scientifically - if POPC/water worked fine, but a POPC/protein/water system doesn't, what's the variable that changed?

Moreover, look at when the failure is happening - it's failing at step zero. LINCS warnings always have the same causes:

1. Wrong .mdp settings (likely not the case, see above)
2. Insufficient equilibration (well, yours is failing outright, so probably not)
3. Insufficient minimization (hmmm...)



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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