[gmx-users] Hello Regarding Lincs error

[Justin Lemkul]

On 9/18/14 6:38 AM, RINU KHATTRI wrote:
> hello
> i am also facing the same problem i worked on the protein complex
> (popc ) but once again i am using same procedure its gives error even
> i changed .mdp file parameters

Changed to what?  From what?

> after running it gives 61%
> mdrun
>
> grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o npt.tpr
>
>   mdrun -nt 4 -deffnm npt

Did previous minimization and/or equilibration runs succeed?

-Justin

> kindly help
>
> On Thu, Sep 18, 2014 at 2:23 PM, Ujwala Patil <ujwalanpatil at gmail.com> wrote:
>> Hello I am doing simulation of   dioxane+ water system
>> during energy minimization i got error
>> Too many LINCS warnings (1337)
>> If you know what you are doing you can adjust the lincs warning threshold
>> in your mdp file
>> or set the environment variable GMX_MAXCONSTRWARN to -1,
>> but normally it is better to fix the problem
>>
>> my em.mdp file is
>>
>> integrator  = steep      ;
>> emtol       = 500.0
>> emstep      = 0.01
>> nsteps      = 500
>>
>> nstlist     = 1.4
>> ns_type     = grid
>> rlist       = 1.0
>> coulombtype = PME
>> rcoulomb    = 1.0
>> rvdw        = 1.4
>> constraints = none
>> pbc         = xyz
>>
>>
>> i have  seen some  similar type of error
>>
>> but not able to fix
>>
>> please help me to solve the problem
>> --
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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