[gmx-users] [EXTERNAL] Lincs warning and Bond length not finite
Smith, Micholas D.
smithmd at ornl.gov
Mon May 4 02:55:55 CEST 2020
How did you set up your graphene sheet originally? Also are you treating the sheet as an infinite sheet (using with periodic molecules)?
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of Mohamed Abdelaal
Sent: Sunday, May 3, 2020 8:40 PM
To: gmx-users at gromacs.org; users at maillist.sys.kth.se
Subject: [EXTERNAL] [gmx-users] Lincs warning and Bond length not finite
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.
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 ?
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