[gmx-users] LINCS crushes

[Yuri Garmay]

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.
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?

Regards,
Yuri.
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