[gmx-users] Pressure coupling problem
Tam, Benjamin
benjamin.tam.14 at ucl.ac.uk
Sat May 25 11:34:03 CEST 2019
Hi Jacob,
Thank you for your responses. My system is set up for generating a polymer with over 40800 atoms. So initially, I need to simulate the system in different pressure in order to set up a "correct" simulation system. I have simulated with Berendsen barostat for 10 ns and through the density and energy plot, I can confirm that the system box size has remained stable. Yet with P-R barostat, the explosion happened with 100 ps and somehow the system can continue to run. There is no restraint or constraint to the atom or to the box. I even check it with a box filled with TIP4P water molecules alone, the box still exploded with P-R.
However, when I changed the version. It seems like the problem are solved, which is rather strange and unbelievable.
Best,
Ben
________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Jacob Monroe <jimonroe at umail.ucsb.edu>
Sent: 24 May 2019 18:56
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Pressure coupling problem
Hi Ben,
I haven’t seen a response yet, so since I’ve encountered this type of thing before, I’ll chime in with my two cents.
I’ve run into similar issues before, and it’s always turned out to be something with the way I set up the simulation. What I’ve found is that if things tend to explode with the Parinello-Rahman barostat, they are also exploding with the Berendsen barostat, just at a slower rate due to the tendency of the latter algorithm to incorrectly over dampen fluctuations. I’ve also found that some simulations stay stable for longer than others simply by chance, but if you run long enough, they will eventually explode as well. My recommendation is to watch the simulation box carefully or plot its dimension over time - if it just keeps growing, now matter how slowly, you have a problem.
Do you have any atoms in the box frozen? Or position restraints with large spring constants? Sometimes restraints for holding two molecules close to each other, depending on the system, can also cause odd behavior. Without knowing more about your system, I’ll also ask, do you actually need a barostat, or will NVT be fine? Or are there ways to relax your system to an appropriate density without seeing the problem behavior?
Best,
Jacob
On May 23, 2019, at 10:23 AM, Tam, Benjamin <benjamin.tam.14 at ucl.ac.uk<mailto:benjamin.tam.14 at ucl.ac.uk>> wrote:
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-bounces at maillist.sys.kth.se<mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se<mailto: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<mailto: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,
Ben
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----------------------------------------
Jacob I Monroe
PhD Candidate
Department of Chemical Engineering
University of California - Santa Barbara
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