[gmx-users] Fwd: [Gmx-plumed Query] - Lincs warnings during meta-dynamics calculation of pyranose sugar using phi and theta as Collective Variables

[Amit Singh]

I am doing meta-dynamics MD simulations of alpha-mannose using
GROMACS-PLUMED software. My collective variables are phi and theta
(Cremer-Pople ring puckering coordinates). But my simulations are
terminating prematurely with following LINCS warnings :


Step 464363, time 464.363 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 3.575117, max 12.384567 (between atoms 8 and 9)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
      8      9  153.0    0.3415   1.4870      0.1111
      8      9  153.0    0.3415   1.4870      0.1111
      8      9  153.0    0.3415   1.4870      0.1111
      8      9  153.0    0.3415   1.4870      0.1111
      8      9  153.0    0.3415   1.4870      0.1111
      8      9  153.0    0.3415   1.4870      0.1111

My system has one alpha-mannose (atom no. 1 to 24) and 590 water molecules.
Respective .mdp file and plumed input file provided below:


*******************************************************************************************
title                   = Production Run
; Run parameters
integrator                                = md        ; leap-frog integrator
nsteps                                     = 50000000    ; 1 * 50000000 =
50000 ps (50 ns)
dt                                            = 0.001     ; 1 fs
; Output control
nstenergy                                = 5000      ; save energies every
5.0 ps
nstlog                                      = 5000      ; update log file
every 5.0 ps
nstxout-compressed               = 5000      ; save compressed coordinates
every 5.0 ps
compressed-x-grps                 = System    ; save the whole system
; Bond parameters
continuation                            = yes       ; Restarting after NPT
constraint_algorithm               = lincs    ; holonomic constraints
constraints                              = h-bonds   ; bonds involving H
are constrained
lincs_iter                                 = 2         ; accuracy of LINCS
lincs_order                              = 4         ; also related to
accuracy
lincs-warnangle                     = 90
; Neighborsearching
cutoff-scheme                       = Verlet    ; Buffered neighbor
searching
ns_type                                 = grid      ; search neighboring
grid cells
nstlist                                    = 20        ; 20 fs, largely
irrelevant with Verlet scheme
rcoulomb                              = 1      ;  short-range electrostatic
cutoff (in nm)
rvdw                                     = 1       ; short-range van der
Waals cutoff (in nm)
; Electrostatics
coulombtype                      = PME       ; Particle Mesh Ewald for
long-range electrostatics
pme_order                         = 4         ; cubic interpolation
fourierspacing                    = 0.5      ; grid spacing for FFT
; Temperature coupling is on
tcoupl                                = v-rescale            ; modified
Berendsen thermostat
tc-grps                               = AMAN Water      ; two coupling
groups - more accurate
tau_t                                  = 0.1       0.1               ; time
constant, in ps
ref_t                                   = 300       300          ;
reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl                                = Berendsen         ;  Pressure
coupling on in NPT
pcoupltype                         = isotropic             ; uniform
scaling of box vectors
tau_p                                  = 1.0                   ; time
constant, in ps
ref_p                                  = 1.0                   ; reference
pressure, in bar
compressibility                   = 4.5e-5                ; isothermal
compressibility of water, bar^-1
; Periodic boundary conditions
pbc                                     = xyz       ; 3-D PBC
; Dispersion correction
DispCorr                            = EnerPres  ; account for cut-off vdW
scheme
; Velocity generation
gen_vel                             = no        ; Velocity generation is off
; Comm removal
comm-mode                      =  Linear
comm-grps                        =  AMAN Water

******************************************************************************************************

Plum.dat file

******************************************************************************************************
# Defining serial number of ring atoms from O5-C1-C2-C3-C4-C5

PUCKERING ATOMS=7,1,8,12,16,5 LABEL=puck

# Deposit a Gaussian every 600 time steps, with initial height equal to 1.0
kJ/mol

metad: METAD ARG=puck.phi,puck.theta SIGMA=0.35,0.35 PACE=600 HEIGHT=1.0
BIASFACTOR=10.0 TEMP=300.0 FILE=HILLS_1

# Print both collective variables and the value of the bias potential on
COLVAR file
PRINT ARG=puck.phi,puck.theta FILE=COLVAR_1 STRIDE=10

*******************************************************************************************************

I had gone through the gromacs web-page (
http://www.gromacs.org/Documentation/Terminology/Blowing_Up) describing the
various steps to overcome the LINCS warnings/errors. I followed all the
steps mentioned therein still not successful in sorting out the error.

>From my own perspective, I think the large rotation in CV (phi, theta)
results in the failure of LINCS algorithm. Is there any way to restrict the
change in collective variable at each step so that the RMS deviation can be
minimized.

Please provide your valuable inputs on this error? Big thanks in advance.


-- 
with regards
Amit Singh
Graduate Research Scholar
Indian Institute of Technology
Gandhinagar, Gujarat, INDIA