[gmx-users] LINCS crushes

[Justin A. Lemkul]

Yuri Garmay wrote:
> Hi, all!
> 
> I am trying to simulate a system of peptide, water, NaCl and DMSO.
> I used pdb2gmx to generate .top file for DMSO and then created this .itp:
> (initial DMSO structure had been minimized before it was used for box 
> generation)
> 
> [ moleculetype ]
> ; Name            nrexcl
> DMSO               3
> 
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass 
>  typeB    chargeB      massB
> ; residue   1 DMSO rtp DMSO q  0.0
>      1      SDmso      1   DMSO  SDmso      1    0.12753      32.06   ; 
> qtot 0.1275
>      2      ODmso      1   DMSO  ODmso      1   -0.44753    15.9994   ; 
> qtot -0.32
>      3      CDmso      1   DMSO  CDms1      1       0.16     15.035   ; 
> qtot -0.16
>      4      CDmso      1   DMSO  CDms2      1       0.16     15.035   ; 
> qtot 0
> 
> [ bonds ]
> ;  ai    aj funct            c0            c1            c2            c3
>     1     2     2    gb_41
>     1     3     2    gb_42
>     1     4     2    gb_42
>     2     3     2    gb_49
>     2     4     2    gb_49
>     3     4     2    gb_50
> 
> Corresponding record 
> in /usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp is:
> 
> [ DMSO ]
>  [ atoms ]
> SDmso SDmso     0.12753     0
> ODmso ODmso    -0.44753     0
> CDms1 CDmso     0.16000     0
> CDms2 CDmso     0.16000     0
>  [ bonds ]
> SDmso ODmso    gb_41   
> SDmso CDms1    gb_42   
> SDmso CDms2    gb_42   
> ODmso CDms1    gb_49   
> ODmso CDms2    gb_49   
> CDms1 CDms2    gb_50   
>  [ angles ]
> ;  ai    aj    ak   gromos type
>  [ impropers ]
> ;  ai    aj    ak    al   gromos type
>  [ dihedrals ]
> ;  ai    aj    ak    al   gromos type
> 
> Then I created box with genbox using -ci and -cs options. I did add 
> following strings in system .top file:
> before [ system ]
> 
> ; Include DMSO topology
> #include "dmso.itp"
> 
> after [ molecules ]
> 
> DMSO             69
> 
> Parameters what I used for energy minimization was:
> 
> ; Parameters describing how to find the neighbors of each atom and how 
> to calculate the interactions
> nstlist = 1 ; Frequency to update the neighbor list and long range forces
> ns_type = grid ; Method to determine neighbor list (simple, grid)
> rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
> coulombtype = PME ; Treatment of long range electrostatic interactions
> pme_order = 4 ; cubic interpolation
> fourierspacing = 0.12 ; grid spacing for FFT
> rcoulomb = 1.0 ; Short-range electrostatic cut-off
> rvdw = 1.0 ; Short-range Van der Waals cut-off
> pbc = xyz ; Periodic Boundary Conditions (yes/no)
> 
> ; Dispersion correction
> DispCorr = EnerPres ; account for cut-off vdW scheme
> 
> 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
> 
> Then I get minimization crushed after such warnings:
> 
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.646692, max 1.998582 (between atoms 237 and 236)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>     223    222  148.1    0.1535   0.0548      0.1530
> 
> When I set constraints = h-bonds minimization was successful.
> 
> It seems LINCS algorithm has limitations on the molecule topology. I 
> didn't know details of this method and need help.

LINCS is actually quite stable, but will crash if the system is not ;)

> What should I do for simulation works? Is there need to change DMSO 
> topology or maybe it is better to use constraints = h-bonds option?
> 

Try minimizing again now with all bonds constrained using the output of the EM 
that ran.  Generally, if EM crashes, your system contains some unresolvable 
clash or inappropriate geometry.  Perhaps you have now relaxed the bad 
interactions sufficiently to proceed.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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