FATAL ERROR: Periodic cell has become too small for original patch grid!

[Gideon Mitchell]

I've encountered the following error several times when running GaMD on
NAMD3 via CUDA:

FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.

Looking at the NAMD mailing list
https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2009-2010/2898.html,
it appears as though this error is due to the system density diverging from
its initial state. Looking at the system trajectory file, it appears as
though the system is being compressed on the z-axis and expanding on x- and
y-axes. This issue only occurs when I run the GaMD equilibration step, and
works fine for cMD.

I've attached a copy of my config file below, as well as the output xst
file so you can see how the periodic boundaries change. Do you know the
cause of this error?

Thank you for your help,
- Gideon

[Yinglong Miao]

Hi Gideon,

Your simulation config file looks ok to me. As for the system density / size change, could you possibly run longer cMD NPT equilibration and then use the “equilibrated” system restart files to continue with GaMD simulation?

You can also test “increase margin, or disable useFlexibleCell for liquid simulation” as suggested in the output.

Best,
Yinglong

Yinglong Miao, Ph.D.
Associate Professor
Computational Medicine Program and
Department of Pharmacology
University of North Carolina - Chapel Hill
Tel: 1-919-962-5696
http://miaolab.org

On Dec 20, 2023, at 9:17 PM, Gideon Mitchell gideonm@users.sourceforge.net wrote:

I've encountered the following error several times when running GaMD on
NAMD3 via CUDA:

FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.

Looking at the NAMD mailing list
https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2009-2010/2898.html https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fnamd%2Fmailing_list%2Fnamd-l.2009-2010%2F2898.html&data=05%7C02%7Cmiao%40ku.edu%7Ccad3975efc1b42d0929c08dc01cb033b%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638387218645916627%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=impxPL%2BxnQkhPU%2FJpQ%2Fk5UDC5dd1VONt1CgpuNbr3Io%3D&reserved=0,
it appears as though this error is due to the system density diverging from
its initial state. Looking at the system trajectory file, it appears as
though the system is being compressed on the z-axis and expanding on x- and
y-axes. This issue only occurs when I run the GaMD equilibration step, and
works fine for cMD.

I've attached a copy of my config file below, as well as the output xst
file so you can see how the periodic boundaries change. Do you know the
cause of this error?

Thank you for your help,
- Gideon

FATAL ERROR: Periodic cell has become too small for original patch grid! https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fp%2Fgamd%2Fdiscussion%2Fgeneral%2Fthread%2F3470636f90%2F%3Flimit%3D25%23b30f&data=05%7C02%7Cmiao%40ku.edu%7Ccad3975efc1b42d0929c08dc01cb033b%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638387218645916627%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=GRIoIPw5K2Bwc0JcpZAigvAkAlEXXlqAuMELtw1xIeo%3D&reserved=0
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[Gideon Mitchell]

Yinglong,

Thank you for your help. We tried running a longer cMD simulation, but got the same results. However, we were able to resolve it by adding a margin of 5 to the NAMD configuration file.

[Yinglong Miao]

Sounds good!

Yinglong