[gmx-users] About Em and Equlibration With Lincs Algorithim

[vidhya sankar]

Dear Justin Than you for your previous Reply  

I am doing EM for My cyclic peptide using following EM. MDP

; ions.mdp - used as input into grompp to generate ions.tpr
; Parameters describing what to do, when to stop and what to save
integrator  = steep    ; Algorithm (steep = steepest descent minimization)
emtol       = 1000    ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep      = 0.01      ; Energy step size
nsteps      = 50000     ; Maximum number of (minimization) steps to perform
constraints = none
; 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       = 1.4       ; Cut-off for making neighbor list (short range forces)
coulombtype = PME       ; Treatment of long range electrostatic interactions
rcoulomb    = 1.4       ; Short-range electrostatic cut-off
rvdw        = 1.4       ; Short-range Van der Waals cut-off
pbc         = xyz       ; Periodic Boundary Conditions

Steepest Descents converged to machine precision in 2885 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -2.88282144376129e+05
Maximum force     =  1.25808872222753e+03 on atom 107
Norm of force     =  4.38175991068554e+01

 i  Have done Five time EM using emtol  = 1000  

Every Attempt became failed Then i planned to use emtol = 1500 

In Previus Mail You Quoted the Possible emtol  = 1000 For Most of Protein in Water  But in My case  it is not so Because the ring is  so stained 

So  I use emtol = 1500 it is converged Successfully as follows

writing lowest energy coordinates.

Steepest Descents converged to Fmax < 1500 in 2868 steps
Potential Energy  = -2.88282144367798e+05
Maximum force     =  1.31510551954873e+03 on atom 107
Norm of force     =  4.39665399153860e+01


If I continue further NPT equlibration with Lincs Algorithim it shows Error aS follows

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 1167.301393, max 4514.205877 (between atoms 164 and 168)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    164    168  154.6    2.3463 690.8265      0.1530
    164    168  154.6    2.3463 690.8265      0.1530
    165    166  118.1    1.3451 224.6411      0.1530
    165    166  118.1    1.3451 224.6411      0.1530
    166    167   67.4    1.1731  86.2422      0.1530
    166    167   67.4    1.1731  86.2422      0.1530
    168    169  141.9    2.9836 281.9632      0.1230
    168    169  141.9    2.9836 281.9632      0.1230
      1      2   66.8    0.0735   2.3215      0.1000
      1    168   59.8    2.7313 251.2519      0.1330
      1      3  126.5    0.1241   2.3286      0.1470
    156    157   96.0    0.1464   0.3827      0.1470
    157    161  110.5    0.1604   0.4095      0.1530
    157    158   95.9    0.1523   0.3563      0.1530
    161    163   31.2    1.3955 148.8536      0.1330
    161    162   81.6    0.1293   0.6410      0.1230
    163    164  137.9    3.2852 517.7200      0.1470
    163    164  137.9    3.2852 517.7200      0.1470
      3     16   92.2    0.1534   2.8760      0.1530
      3      4   93.9    0.1528   2.8694      0.1530

Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.1#

Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.1#
Wrote pdb files with previous and current coordinates
starting mdrun 'L-22 CYCLIC PEPTIDE'
100000 steps,     20.0 ps.
Warning: 1-4 interaction between 166 and 168 at distance 2.841 which is larger than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size


step 0: Water molecule starting at atom 7007 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
    124    125  111.2    0.1530 297.2103      0.1530
    125    127   38.3    0.1530   0.1981      0.1530
    121    123   98.7    0.1470 1978.8023      0.1470
    119    121  139.2    0.1330 222.7882      0.1330
    119    120   35.3    0.1230   0.1629      0.1230
    106    119   33.3    0.1530   0.1945      0.1530

step 0: Water molecule starting at atom 6461 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#



step 0: Water molecule starting at atom 2855 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.2#
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates


How TO Rectify the  above errror Even I  I have Visualised the EM.gro file in VMD It seem to be good (it Indicates That topology is correct)  Must I use Lincs Algorithim During NPT Equlibration If I Run Without LINCS It runs Sucessfully 


Thanks in advance