Dear all, To follow through with this email. It seems like the barostat problem comes from a different version. As I tested with version gromacs/2016.3/intel-2017-update1, the system remains stable for 1 ns and the same system explode with gromacs/2018.3/intel-2018.
Was there some kind of bug in the newer version or am I missing something? Best, Ben -----Original Message----- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of Tam, Benjamin Sent: 23 May 2019 11:40 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Pressure coupling problem Dear Gromacs user, Currently, I am baffled about a simulation that I am running and I hope I will find some answer here. Initially, I have run my system with Berendsen barostat to equilibrate for 1 ns. The system looks fine as there is no box explosion. However, after the equilibration, I change the barostat to Parinello-Rahman. The box exploded. I tried to debug my system by turning off Lennard Jones and charge (separately and together). Yet the box still explodes without any reason. The system is set as 300K and 1 bar. Here, I have to mention that the intramolecular bond is correct as the molecules did not explode. The only difference is the barostat that I have varied. Therefore, can anyone give me some clue what is going and why changing the barostat will cause this effect? Thank you very much. Best regards, Ben -- Gromacs Users mailing list * Please search the archive at https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&data=02%7C01%7Cbenjamin.tam.14%40ucl.ac.uk%7C2022b359b3f24cd3d08c08d6df6b00dc%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636942048005761630&sdata=1hR5oB0Fa7wLHJ29jk58%2BJiaaxPYdtHD%2FkWe69xUPG4%3D&reserved=0 before posting! * Can't post? Read https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists&data=02%7C01%7Cbenjamin.tam.14%40ucl.ac.uk%7C2022b359b3f24cd3d08c08d6df6b00dc%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636942048005761630&sdata=oZ7F8v2ixGx2g%2FfVT68BvAx%2BKvqzWUIN3Zs0m4HSaig%3D&reserved=0 * For (un)subscribe requests visit https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-users&data=02%7C01%7Cbenjamin.tam.14%40ucl.ac.uk%7C2022b359b3f24cd3d08c08d6df6b00dc%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636942048005761630&sdata=LuhMwqGuFNA0S7V1JeeuS%2FVWVL45DrOasYO7LSWXwnY%3D&reserved=0 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.
