[gmx-users] Problem of lincs in free energy calculations

[Александр Лашков]

Usually, in this case, Lincs algorithm is not the cause of unstable MD
simulation. It is symptome of possible blowing up. Possible reasons are
described here http://www.gromacs.org/Documentation/Terminology/Blowing_Up
Alex

ср, 22 янв. 2020 г. в 12:57, Sadaf Rani <sadafrani6 at gmail.com>:

> Dear Gromacs users
> During free energy calculation, I am getting lincs warning at MD run in
> some of Lambda windows. To cope with this I have reduced my time step to 1
> fs rather than 2. Some of them converged but for others, it still gives
> lincs warning and generates different PDB structures. If the initial
> topology had some issue it should not work for any system.
> Could you please suggest me how should I fix this error?
>
> Thanks
>
> Sadaf Rani
> Ph.D. visiting student
> Lancaster University
> United kingdom
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