How did you set up your graphene sheet originally? Also are you treating the sheet as an infinite sheet (using with periodic molecules)?
-Micholas -----Original Message----- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of Mohamed Abdelaal Sent: Sunday, May 3, 2020 8:40 PM To: gmx-us...@gromacs.org; us...@maillist.sys.kth.se Subject: [EXTERNAL] [gmx-users] Lincs warning and Bond length not finite 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/1yyUJNg4yXnPfsxZ9gQ4LV5sqRKnJq9rF 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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
