[gmx-users] LINC warning after long time simulations

[Miguel Machuqueiro]

Hi,
This is most probably due to Reaction-Field. The moment you add 
peptides/proteins to the system, you will have hydrogens atoms and those 
are the ones giving the LINCS warnings.

If you want to continue using RF in your setup, you need to downgrade to 
GMX version 4.0.x.

For more information, check out this thread:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2011-December/005489.html

Best,
M.

On 01/12/2015 12:45, Justin Lemkul wrote:
>
>
> On 11/30/15 5:01 PM, 凌未风 wrote:
>> Hi All:
>>
>> I pasted this once several days ago but no one replied. I know there
>> are a lot of questions in the forum regarding LINC warning, but my
>> problem seems quite strange. So I write here again.
>>
>> My simulation system contains lipids and proteins, I am using
>> gromos53a6 for the proteins and reaction field to deal with the long
>> range electrostatic interactions for some reason.
>> My systems keep on complaining about LINC warning, such as some angle
>> rotated more than 30 degrees, after very long simulations (one after
>> 140 ns simulations, the other after 450 ns simulations).
>> I searched the website of gromacs regarding blowing up as well as the
>> forum for discussions, however, my problem seemed not because of bad
>> initial conformation or unreasonable pressure or temperature coupling.
>> I suspect if the problem is due to the topologies of the lipids I was
>> using, because the topologies of lipids were built by myself. So I
>> also run simulations of single lipids in solution and the topology
>> works fine.
>> So I am really confused.
>> I really appreciate if anyone could give me some suggestions
>> regarding this strange problem. Is it ok to set the GMX_CONSTRWARN to
>> -1 or I should do something else to solve this problem.
>>
>
> You should never ignore LINCS warnings. They indicate a fundamental
> instability in the system. If the simulation goes for a long time,
> this just indicates that you have a subtle problem (probably in the
> topology or somewhere in the .mdp settings) that leads to an invalid
> physical model.
>
> -Justin
>

-- 
============================================
Miguel Machuqueiro
Center of Chemistry and Biochemistry
Faculty of Sciences, University of Lisbon
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1749-016 Lisboa, Portugal
Tel.  : +351 217500112 (int.ext.28552)
Mobile: +351 967562285
E-mail: machuque at ciencias.ulisboa.pt
www1: http://webpages.fc.ul.pt/~mamachuqueiro
www2: http://intheochem.fc.ul.pt
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