[gmx-users] Pressure coupling problem

Tam, Benjamin benjamin.tam.14 at ucl.ac.uk
Thu May 23 19:23:07 CEST 2019

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? 


-----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 Tam, Benjamin
Sent: 23 May 2019 11:40
To: gromacs.org_gmx-users at 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,

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&amp;data=02%7C01%7Cbenjamin.tam.14%40ucl.ac.uk%7C2022b359b3f24cd3d08c08d6df6b00dc%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636942048005761630&amp;sdata=1hR5oB0Fa7wLHJ29jk58%2BJiaaxPYdtHD%2FkWe69xUPG4%3D&amp;reserved=0 before posting!

* Can't post? Read https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists&amp;data=02%7C01%7Cbenjamin.tam.14%40ucl.ac.uk%7C2022b359b3f24cd3d08c08d6df6b00dc%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636942048005761630&amp;sdata=oZ7F8v2ixGx2g%2FfVT68BvAx%2BKvqzWUIN3Zs0m4HSaig%3D&amp;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&amp;data=02%7C01%7Cbenjamin.tam.14%40ucl.ac.uk%7C2022b359b3f24cd3d08c08d6df6b00dc%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636942048005761630&amp;sdata=LuhMwqGuFNA0S7V1JeeuS%2FVWVL45DrOasYO7LSWXwnY%3D&amp;reserved=0 or send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list