[gmx-users] about md simulation

[amri ta]

Dear colleagues,
 
 I am simulating a phosphorylated protein embedded in waterbox. 
When I try running mdrun, I get a LINCS warning.
 
Does this mean that I have go back to the CG-EM step and use the double 
precision libs?

The md.log file reads:

...
Initializing LINear Constraint Solver
  number of constraints is 2365
  average number of constraints coupled to one constraint is 2.5

   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.336565   691       696   0.033770
        After LINCS         0.342830    698        700   0.028042


Step -2, time -0.004 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.342830 (between atoms 698 and 700) rms 0.028042
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    687   689      34.6    0.1776    0.1937     0.1330
    689   690      34.7    0.1079   0.0919      0.1000
   --------------------------------------------------
Constraining the coordinates at t0-dt (step -1)
   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.095785   3223   3224   0.006243
        After LINCS         0.858278   3397   3398   0.016634


Step -1, time -0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.858278 (between atoms 3397 and 3398) rms 0.016634
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   3395   3398   76.2    0.1341   0.0446      0.1470
   3398   3399   78.8    0.1341   0.0492      0.1470
Constraint error in algorithm Lincs at step -1
Started mdrun on node 0 Tue Sep 11 07:03:49 2007

Initial temperature: 420.799 K

           Step           Time         Lambda      
              0        0.00000        0.00000        

Grid: 10 x 10 x 10 cells
Configuring nonbonded kernels....
Testing x86_64 SSE supports...presents
           
   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         70.089874   1537   1456   0.559021
        After LINCS         29.983810   3223   3224    0.787549


Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 227.983810 (between atoms 3223 and 3224) rms 4.787549
atom 1 atom 2  angle  previous, current, constraint length
   3395   3398   76.2    0.1341   0.0446      0.1470
   3398   3399   78.8    0.1341   0.0492      0.1470

Constraint error in algorithm Lincs at step 0

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 227.983810 (between atoms 3223 and 3224) rms 4.787549
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
   3395   3398   76.2    0.1341   0.0446      0.1470
   3398   3399   78.8    0.1341   0.0492      0.1470

Constraint error in algorithm Lincs at step 1
 and the simulation stops at step 1.

 Do I have to modify my md.mdp to remedy this?
 
 Your advice is appreciated.
 
 Best regards,

Amrita Ghosh
National Institute of Mental Health and Neurosciences,
Bangalore-29.
India.
----------------------------------------------------------------------------------------------------------------------

title               =  Full mdp run sample
cpp                 =  /lib/cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
steps              =  2000000000 ; total 100 ns
;nstcomm             =  1
nstxout             =  500
nstvout             =  1000
nstfout             =  0
nstlog              =  500
nstenergy           =  500
nstlist             =  10
ns_type             =  grid
rlist               =  0.9
coulombtype         =  PME
rcoulomb            =  0.9
rvdw                =  1.4
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tau_t               =  0.1      0.1     0.1
tc-grps             =  protein  sol   NA+
ref_t               =  300      300     300
; Energy monitoring
energygrps          =  protein  sol   NA+
; Pressure coupling is on
Pcoupl              =  berendsen
pcoupltype          =  anisotropic
tau_p               =    0.5  
compressibility     =  4.5e-5   
ref_p               =  1.0      
; Generate velocites is on at 300 K.
gen_vel             =  no
gen_temp            =  300.0
gen_seed            =  173529


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