[gmx-users] A charge group moved too... during backward transition of dual topologies
Nash, Anthony
a.nash at ucl.ac.uk
Thu Aug 4 09:14:57 CEST 2016
I have tried equilibrating the non-posres simulation for an additional 2.5
ns, and taken just the final frame and velocity (so the timestep 5 5ns).
I’m also recorded a lot more to the output and I extended the fast
transition run from 100ps to 200ps so the change in softcore potentials
are not so extreme. Please note, this only happens in the reverse
transition of the dual topology, and only when I activate delta_lambda. I
end up seeing this:
Not all bonded interactions have been properly assigned to the domain
decomposition cells
A list of missing interactions:
Angle of 14160 missing 3
Proper Dih. of 9958 missing 3
LJ-14 of 2214 missing 4
exclusions of 91790 missing 8
Molecule type 'Protein2'
the first 10 missing interactions, except for exclusions:
Proper Dih. atoms 40 43 49 52 global 63484 63487 63493
63496
LJ-14 atoms 40 52 global 63484 63496
Angle atoms 43 49 52 global 63487 63493 63496
Proper Dih. atoms 44 43 49 52 global 63488 63487 63493
63496
LJ-14 atoms 44 52 global 63488 63496
Proper Dih. atoms 45 43 49 52 global 63489 63487 63493
63496
LJ-14 atoms 45 52 global 63489 63496
Angle atoms 50 49 52 global 63494 63493 63496
Angle atoms 51 49 52 global 63495 63493 63496
LJ-14 atoms 52 55 global 63496 63499
-------------------------------------------------------
Program mdrun_mpi_d, VERSION 5.0
Source code file:
/home/sacat2/gromacs_source/gromacs-5.0/src/gromacs/mdlib/domdec_top.c,
line: 394
Fatal error:
18 of the 130046 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance
(0.934022 nm) or the two-body cut-off distance (1.42 nm), see option -rdd,
for pairs and tabulated bonds also see option -ddcheck
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Dr Anthony Nash
Department of Chemistry
University College London
On 03/08/2016 08:11, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
behalf of Nash, Anthony"
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
a.nash at ucl.ac.uk> wrote:
>Hi all,
>
>I¹m performing free energy calculations based on Crooks Fluctuation
>Theorem. To do this I¹ve used PMX to implement a dual topology. To keep
>things simple, it is a transmembrane polyleucine helical protein where one
>leucine is transforming into a serine - then there is the backward
>transition of serine into Leucine, required for the overlap of two
>gaussian distributions (forward and backward).
>
>I have a very complicated arrangement of steps to equilibrate the system,
>in very brief I have only included those involved once the protein is
>embedded in the bilayer (bilayer eq was around 40 ns over various stages).
>For a backward eq (serine->leucine) I used the parameters:
>
>free_energy = yes
>init_lambda = 1 ;0=forward 1=backward
>delta_lambda = 0 ;equilibrium
>nstdhdl = 1
>sc-coul = yes
>sc-alpha - 0.3
>sc-sigma = 0.25
>sc-power = 1
>
>
>And the eq steps:
>
>-Steepest descent (<100 kjmol threshold)
>-NVT 100ps (carbon-alpha posres 1000 kjmol)
>-NPT 100ps (carbon-alpha posres 1000 kjmol - Berendsen pressure)
>-NPT 10ns (carbon-alpha posres 1000 kjmol - PR pressure)
>-NPT 2.5 ns (turn OFF posres)
>
>The above steps produce a system with serine in the polyleu. I then
>discard the first 1.5 ns and take 10 sets of coordinates and velocities
>from the last 1ns. This is for my Œfast¹ backward (serine->leucine) 100 ps
>transformation using the MDP parameters:
>
>free_energy = yes
>init_lambda = 1 ;0=forward 1=backward
>delta_lambda = -0.00002 ;transitions
>nstdhdl = 1
>sc-coul = yes
>sc-alpha - 0.3
>sc-sigma = 0.25
>sc-power = 1
>
>
>When I run the 10 Œfast¹ transition production runs approximately half of
>them immediately result in the error:
>
>Step 5:
>The charge group starting at atom 63445 moved more than the distance
>allowed by the domain decomposition (1.420000) in direction Z
>distance out of cell 70.681579
>Old coordinates: -48.465 256.312 81.655
>New coordinates: -48.465 256.312 81.655
>Old cell boundaries in direction Z: 5.728 10.974
>New cell boundaries in direction Z: 5.728 10.974
>
>
>-------------------------------------------------------
>Program mdrun_mpi_d, VERSION 5.0
>Source code file:
>/home/sacat2/gromacs_source/gromacs-5.0/src/gromacs/mdlib/domdec.c, line:
>4380
>
>
>Fatal error:
>A charge group moved too far between two domain decomposition steps
>This usually means that your system is not well equilibrated
>For more information and tips for troubleshooting, please check the
>GROMACS
>website at http://www.gromacs.org/Documentation/Errors
>-------------------------------------------------------
>
>
>I understand what this error means, but I was wondering whether I was
>doing something far more fundamentally wrong, given that every forward
>transition (same eq set up, just using init_lambda = 0 and delta_lambda =
>0.00002) never produce this error! They always work, and monitoring my
>work gives me an amazing gaussian distribution.
>
>I have put the 2.5ns production run with no position restraints up for a
>further 2.5 ns, and I¹m testing whether frames from the last ns produce
>similar errors i.e., does the inclusion of serine require further
>equilibration.
>
>I would appreciate any thoughts.
>
>Many thanks
>Anthony
>
>
>
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