[gmx-users] About Lincs Algorithim for Cyclic Peptide

[Justin Lemkul]

On 10/8/12 11:17 AM, vidhya sankar wrote:
> 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
>

Your system is insufficiently minimized, a value of Fmax < 1000 is generally 
acceptable for most protein-in-water systems.  Probably you have a bad starting 
geometry that is being forced to do something nasty when you impart a bond 
between the termini.  In any case, you can find out by visualization what atom 
17042 is and what its problem might be.

-Justin

>
> 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
>

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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