[gmx-users] LINCS warning and segmentation fault for methane in 1-octanol simulation

[Justin A. Lemkul]

vivek sharma wrote:
> Hi There,
>  I was trying to run a equilibrium run (npt) for system of "Methane in 
> 1-octanol" (1 methane molecule with 200 1-octanol molecules with OPLS FF 
> parameters). Following is the series of steps I followed:
> 1. Energy minimization with steep integrator for 5000 steps
> 2. Energy minimization with l-bfgs integrator for 5000 steps
> 3. NVT run for 100 ps with sd integrator
> 4. NPT run for 100 ps with sd integrator (with Pcoupl = 
> Parrinello-Rahman, tau_p = 0.5, compressibility = 4.5e-05, ref_p = 1.0)
> 
> During the NPT run I am ending up with following error (too many LINCS 
> warning):
> ---------------------------------------------
> Step 25406, time 50.812 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 11.778495, max 363.475445 (between atoms 2158 and 2157)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    2152   2150   90.0    0.1090   1.3690      0.1090
>    2152   2151   90.0    0.1090  36.5266      0.1090
>    2158   2156   90.0    0.1091   0.5637      0.1090
>    2158   2157   90.0    0.2349  39.7278      0.1090
> 
> Back Off! I just backed up step25406b_n0.pdb to ./#step25406b_n0.pdb.1#
> 
> Back Off! I just backed up step25406c_n0.pdb to ./#step25406c_n0.pdb.1#
> Wrote pdb files with previous and current coordinates
> Segmentation fault
> ------------------------------------------------------------
> 
> *.mdp files for above simulation are adapted from tutorial on free 
> energy calculation by Justin.
> 
> Please suggest me what could be wrong with above simulation.
> 

The answer for LINCS warnings is always the same - the system has become 
unstable due to inappropriate geometry, bad .mdp settings, or a combination of 
both.  To troubleshoot, start by turning off the free energy code to make sure 
your system is actually stable.  If it's not, refer here:

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

If it is stable, turn back on whatever free energy settings you're using. I 
assume, based on the tutorial, that this is a simple vdW transformation?

-Justin

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

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

========================================