[gmx-users] LINCS WARNING - Protein-Membrane-system

[Shima Arasteh]

Thanks.
I compared settings of mdp files in POPC/WATER and POPC/PROTEIN/WATER systems. The only difference I found between them was about the bonds constraints. The constraints of mdp file for POPC/WATER was  "constraints  = h-bonds ", however it was "constraints = all-bonds" for POPC/PROTEIN/WATER system. 

You say insufficient minimization, I don't think so........ . I got a sensible potential energy as follow:
Potential Energy  = -1.2414742e+06
Maximum force     =  9.8055229e+01 on atom 4719
Norm of force     =  3.4904923e+00
Then what's wrong with the EM?



 
Sincerely,
Shima


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Tuesday, January 1, 2013 6:45 PM
Subject: Re: [gmx-users] LINCS WARNING - Protein-Membrane-system



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

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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