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

[Mark Abraham]

On 10/02/2012 4:41 PM, vivek sharma wrote:
> Hi Justin,
> Thanks for your response. After posting my query, I tried running the
> similar set with
>   NPT run for 100 ps with sd integrator (with Pcoupl = berensen, tau_p
> = 0.5, compressibility = 4.5e-05, ref_p = 1.0)
> On giving berendsen instead of Parrinello-Rahman for pressure
> coupling, job finished successfully. Can you comment on this?

I suggest you read the manual section on pressure coupling, which likely 
explains this observation.

Mark

> As par the tutorial I am using simple vdW transformation only as mentioned below
> ---------
> couple-moltype           = Methane  ; name of moleculetype to decouple
> couple-lambda0           = vdw      ; only van der Waals interactions
> couple-lambda1           = none     ; turn off everything, in this case only vdW
> ---------
>
> Thanks,
> Vivek
>
> On 09/02/2012, Justin A. Lemkul<jalemkul at vt.edu>  wrote:
>>
>> 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
>>
>> ========================================
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