[gmx-users] [EXTERNAL] Re: Lincs warning and Bond length not finite

Smith, Micholas D. smithmd at ornl.gov
Mon May 4 03:31:25 CEST 2020

OPLS tends to be a common choice for graphene. That being said, if you really want to use gromos (for some reason), be sure (as Alex has stated) to make sure that the graphene edges match across the PBC otherwise do not use PBC (but then be sure to change your electrostatics appropriately and make sure the sheet is sufficiently large). 


-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of Alex
Sent: Sunday, May 3, 2020 9:04 PM
To: gmx-users at gromacs.org
Subject: [EXTERNAL] Re: [gmx-users] Lincs warning and Bond length not finite

You have pressure scaling and LINCS convergence issues, suggesting that the starting configuration is far from equilibrium, as well as potentially other issues.

Gromos FF is not appropriate for graphene, and neither is turning C-C bonds into LINCS constraints, as set by your 'all-bonds' -- graphene is not a small organic molecule or a protein. Also, if your system is periodic in all directions, make sure the graphene edges are crystallographically commensurate with respect to PBC and the box size is appropriate. Finally, make sure that the small molecules you're depositing on graphene are properly pre-equilibrated.


On 5/3/2020 6:39 PM, Mohamed Abdelaal wrote:
> Hello everyone,
> I am simulating  the evaporation of non protein molecules on a 
> graphene sheet. I am using gromos force field and hence the lincs 
> constrain are set to all-bonds.  I have done the energy minimization 
> and NVT successfully without any warnings. During the NPT 
> equilibiration I got Lincs warning but the NPT equilibiration was 
> completed to the end. During the md production run, I received lincs 
> warning and Bond length not finite and sometimes I received " 
> nonbonded interaction between particles is larger than the table limit 2.437 nm".
> I have read that this means that my system is blowing up. Hence, I 
> have read the Blowing up and diagnosing unstable system  on gromacs 
> website, I can't recognize  any of the posted issues in my 
> files/simulation and hence,  I can't decide what exactly is the 
> problem or what should I change (it seems that my system is well 
> minimized and the temperature and pressure looks fine). I have added 
> in the below link, the NPT and md logs  and .mdp files and pictures 
> for the potential energy, Temperature, Pressure and Density.
> https://drive.google.com/drive/folders/1yyUJNg4yXnPfsxZ9gQ4LV5sqRKnJq9
> rF
> I have tried the simulation again with none as  lincs constrains and 
> it worked without any errors.
> I think the problem has something to do with the pressure since the 
> problem started during the NPT, but I don't know how exactly to find the problem.
> Can anyone guide me please what should I change or how should I start ?
> Thanks,
> Mohamed
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