Re: AW: AW: Periodic cell has become too small for original patch grid

From: Rohit Modee (rohit.modee_at_research.iiit.ac.in)
Date: Wed Aug 15 2018 - 06:06:12 CDT

what happens when in the first run the replica at higher temperature exchanges with lower temperature. box will shrink in this case too so why is it not giving error.

Regards,
Rohit

----- Original Message -----
From: "Norman Geist" <norman.geist_at_uni-greifswald.de>
To: namd-l_at_ks.uiuc.edu, "Rohit Modee" <rohit.modee_at_research.iiit.ac.in>
Sent: Wednesday, August 15, 2018 4:22:38 PM
Subject: AW: AW: namd-l: Periodic cell has become too small for original patch grid

The error message you see is basically related to NAMDs domain decomposition. The box is departed into patches, which are then distributed across workers in order to accelerate the computation based on parallelization. This decomposition is only done at NAMDs startup. So it's not a problem if the box expands after this initialization, but if it shrinks too much.

Assuming you are using a usual temperature range for REMD, what do you think will happen to your cell at temperatures above the boiling point of water? Yes, the box size expands to a very large number. At the 1st run this is not a problem for NAMD to continue since the initialization was done before, although it doesn't make physical sense for your REMD, IMHO. At the 2nd run, NAMD initializes very different domain decompositions across the replicas, since some of them already have the huge box. If such a replica now exchanges to a lower temperature, the box shrinks a lot and NAMD aborts with the respective message.

How to solve this now? Well, I personally used a temperature dependent target pressure computed from the ANTOINE equation multiplied by three. The supplements include my the REMD code with the respective changes https://pubs.acs.org/doi/10.1021/acs.jpcb.8b05178

Another option is: 1. Pre-equilibrate the cell to the base temperature and disable NPT during the REMD. Depending on the dimensions of the expected conformational changes of your solute, using NPT might be required or not. A small solute will probably work without NPT just fine, since conformational changes will not suppress too much water so that the overall density in your cell will not rise significantly.

Best of luck
Norman Geist

> -----Urspr√ľngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Rohit Modee
> Gesendet: Mittwoch, 15. August 2018 11:35
> An: Norman Geist <norman.geist_at_uni-greifswald.de>
> Cc: namd-l_at_ks.uiuc.edu
> Betreff: Re: AW: namd-l: Periodic cell has become too small for original patch
> grid
>
> yes, I am doing NPT REMD.
>
> langevinPistonTarget 1.01325
>
> dimesnsions of box
> # Periodic Boundary Conditions
> cellBasisVector1 51.579999923706055 0 0
> cellBasisVector2 0 51.4640007019043 0
> cellBasisVector3 0 0 51.75699996948242
> cellOrigin 0.225006103515625 0.10952535271644592 -0.10641514509916306
>
> MARGIN 1.0
> PMEGridSpacing 1.0
>
> ----- Original Message -----
> From: "Norman Geist" <norman.geist_at_uni-greifswald.de>
> To: namd-l_at_ks.uiuc.edu, "Rohit Modee" <rohit.modee_at_research.iiit.ac.in>
> Sent: Tuesday, August 14, 2018 11:58:06 AM
> Subject: AW: namd-l: Periodic cell has become too small for original patch grid
>
> Are you doing NPT remd?
> What target pressure are you using?
> What are the box dimensions?
>
> > -----Urspr√ľngliche Nachricht-----
> > Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> > Auftrag von Rohit Modee
> > Gesendet: Montag, 13. August 2018 10:26
> > An: namd-l_at_ks.uiuc.edu
> > Betreff: namd-l: Periodic cell has become too small for original patch grid
> >
> > Dear All,
> >
> > I am running REMD simulations. have divided 100 ns into 5 jobs of 20 ns
> each.
> > my job0 of 20 ns is complete but when i start job1 from checkpoint files
> from
> > job0 it gives me following error at 22ns
> > Reason: REPLICA 9 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.
> >
> > can some one please explain what this error technically means.
> >
> > i am already using margin of 1 A my water box is cubic with l=50 A
> >
> > in log file i get this value "PME GRID DIMENSIONS 54 54 54" why is this
> 54
> > instead of 50.
> >
> > what effect will it have if
> > 1. I restart job1 with margin as more than 1.
> >
> > regards,
> > Rohit

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