[gmx-users] LINCS WARNING

[Vy Phan]

Dear Justin,
I am so thankful for you kindly reply. Now, I can solve this problem.

Tuong Vy

On Tue, Oct 6, 2015 at 11:49 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/6/15 3:26 AM, Vy Phan wrote:
>
>> Dear all gromacs Users!
>> I want to run a simulation with the system protein-ligand (I have several
>> ligands).
>> With EM, nvt, npt step I put position restraint for the ligands and all
>> thing was fine. After that, I run production simulation without position
>> restraint of ligands. I saw the ligand move out of the initial position
>> and
>> simulation was stopped.
>>
>> Did the LINCS warning  happen because this system is not stable ?
>>
>
> Yes.
>
> How can I keep the continuous running simulation without the  LINCS
>> warnings? I want  the ligands are free to move and find their binding
>> sites.
>>
>>
> Either your ligand topology is not stable or your run settings are not
> sensible.  Please see any of the million or so posts in the gmx-users
> mailing list archive regarding similar or identical situations.
>
> -Justin
>
> This is the warnings:
>> Too many LINCS warnings (1000)
>> 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
>>
>> Thank you so much for any suggestions
>> Tuong Vy
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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