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

[vivek sharma]

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?
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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