[gmx-users] About Lincs Algorithim for Cyclic Peptide

[vidhya sankar]

Dear Justin Thank you For your Previous reply

   I have used the EM.gro file of Cyclic Peptide  For NPT Equlibrartion Without using  Lincs Algorithim it run Suceesfully 
But with Lincs Algorithm It shows Errror As follows Though  I have reduce the time step   
 
relative constraint deviation after LINCS:
rms 3069855679.355833, max 11186146428.941977 (between atoms 164 and 165)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    166    167  143.7    0.1935 179340257.0542      0.1530
    166    167  143.7    0.1935 179340257.0542      0.1530
    168    169  158.7    1.4560 636653487.7409      0.1230
    168    169  158.7    1.4560 636653487.7409      0.1230
    164    168  171.7    2.0007 1704071509.3304      0.1530
    164    165  169.7    1.8838 1711480403.7811      0.1530
    164    168  171.7    2.0007 1704071509.3304      0.1530
    164    165  169.7    1.8838 1711480403.7811      0.1530
    165    166  165.2    0.6922 762944969.2944      0.1530
    165    166  165.2    0.6922 762944969.2944      0.1530
      1      2  139.5    0.1011 1465776.5396      0.1000
      1    168  169.4    1.1190 546331954.5273      0.1330
    145    147   38.1    0.1330   0.1781      0.1330
   
step 0: Water molecule starting at atom 7265 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.2#
Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.2#
Wrote pdb files with previous and current coordinates
Segmentation fault

  Normally The Gromacs Does Not Have terminal option for cyclic Peptide While constructing  .top for Cyclic Peptide (By using pdb2gmx) As Advised By mark I  Have Edited My  initial pdb file final .top file compatible to cyclic Peptide (by Making Bond  between first and Last residue And then Making proper angle,Dihedral and other factors)  
Now I am confident on that topology . Also Bond Between First and Last Residue Are Intact throughout  Entire Dynamics ( Here I am Running Without Lincs Algorithm)

My Question is
  Is it Reasonable and Meaningful To equilibrate And  do Production MD  Without Lincs  otherwise 
Is My EM  Not well Enough ? Because I am doing Three Cycles of EM Output is as follows
Steepest Descents converged to Fmax < 6800 in 2 steps
Potential Energy  = -2.08749539864389e+05
Maximum force     =  6.52976950643761e+03 on atom 17042
Norm of force     =  4.52145850945473e+02 
But When I Equilibrate With Lincs still  It Shows Bad contacts As Mentioned Above  


My NPT.mdp file are as follows
title       = NPT Equilibration 
define      = -DPOSRES          ; position restrain the protein
; Run parameters
integrator  = md                ; leap-frog integrator
nsteps      = 100000            ; 2 * 50000 = 100 ps
dt          = 0.0002             ; 2 fs
; Output control
nstxout     = 1000              ; save coordinates every 2 ps
nstvout     = 1000              ; save velocities every 2 ps
nstenergy   = 1000              ; save energies every 2 ps
nstlog      = 1000              ; update log file every 2 ps
; Bond parameters
continuation         = no        ; Initial simulation 
constraint_algorithm = lincs     ; holonomic constraints 
constraints          = all-bonds ; all bonds (even heavy atom-H bonds) constrained
;lincs_iter           = 1         ; accuracy of LINCS
;lincs_order          = 4         ; also related to accuracy
; Neighborsearching
ns_type     = grid              ; search neighboring grid cels
nstlist     = 5                 ; 10 fs
rlist       = 1.4               ; short-range neighborlist cutoff (in nm)
rcoulomb    = 1.4               ; short-range electrostatic cutoff (in nm)
rvdw        = 1.4               ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype     = PME       ; Particle Mesh Ewald for long-range electrostatics
pme_order       = 4             ; cubic interpolation
fourierspacing  = 0.16          ; grid spacing for FFT
; Temperature coupling is on
tcoupl      = V-rescale             ; Weak coupling for initial equilibration 
tc-grps     = Protein   Non-Protein ; two coupling groups - more accurate
tau_t       = 0.1       0.1         ; time constant, in ps
ref_t       = 310       310         ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl              = Berendsen     ; Pressure coupling on in NPT, also weak coupling
pcoupltype          = isotropic     ; uniform scaling of x-y-z box vectors
tau_p               = 2.0           ; time constant, in ps
ref_p               = 1.0           ; reference pressure (in bar)
compressibility     = 4.5e-5        ; isothermal compressibility, bar^-1
; Periodic boundary conditions
pbc     = xyz                   ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres          ; account for cut-off vdW scheme
; Velocity generation
gen_vel     = yes               ; Velocity generation is on
gen_temp    = 310               ; temperature for velocity generation
gen_seed    = -1                ; random seed
; COM motion removal
; These options remove COM motion of the system
nstcomm         = 10
comm-mode       = Linear
comm-grps       = System 



Thanks In Advance