[gmx-users] peptide insertion in lipid bilayer

[Moutusi Manna]

Dear Justin,
                 i am trying to insert a peptide in trans-bialyer orientation into a pre-equilibrated POPC bilayer using  inflategro script. After 13 steps of compression, the area per lipid is 2.61956768363491 nm^2, whereas the desired area per lipid is 0.658 nm^2. But when i try to energy minimize the compressed structure after 13th steps of compression, the energy did not converged and give the following errors. During em i use strong position restraints on peptide heavy atom using force constants of 100000.
------------------------------
perl inflategro em_13.gro 0.95 POPC 0 com_13.gro 5 area_lip.dat 
grompp -f enermin.mdp -c com_13.gro -p system.top -o em_14.tpr
mdrun -s em_14.tpr -nice 4 -o em_14 -c em_14 -e em_14 -g em_14&
Reading file em_14.tpr, VERSION 3.3.1 (single precision)
Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =        50000

Step 9, time 0.018 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.001381 (between atoms 72 and 74) rms 0.000054
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    539    540   35.7    0.1000   0.1000      0.1000

Step 15, time 0.03 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.003842 (between atoms 65 and 68) rms 0.000141
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    539    540   38.3    0.1000   0.1000      0.1000

Step 16, time 0.032 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.016511 (between atoms 65 and 68) rms 0.000550
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
     65     66   42.8    0.1390   0.1412      0.1390
     65     68   42.9    0.1390   0.1413      0.1390
     66     70   41.9    0.1390   0.1411      0.1390
     68     72   41.1    0.1390   0.1411      0.1390
     70     74   39.6    0.1390   0.1407      0.1390
     72     74   38.7    0.1390   0.1406      0.1390
    344    345   34.8    0.1390   0.1397      0.1390
    344    347   34.4    0.1390   0.1397      0.1390
    345    349   33.6    0.1390   0.1397      0.1390
    347    351   33.1    0.1390   0.1397      0.1390
    349    353   32.7    0.1390   0.1397      0.1390
    351    353   32.6    0.1390   0.1397      0.1390
    381    382   33.3    0.1390   0.1396      0.1390
    381    384   33.5    0.1390   0.1396      0.1390
    382    386   32.9    0.1390   0.1396      0.1390
    384    388   33.2    0.1390   0.1396      0.1390
    386    390   32.4    0.1390   0.1396      0.1390
    388    390   32.5    0.1390   0.1396      0.1390
    539    540   49.3    0.1000   0.1000      0.1000
    546    547   33.5    0.1250   0.1250      0.1250

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 43 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -1.2865473e+05
Maximum force     =  4.7082656e+04 on atom 547
Norm of force     =  6.7057188e+04

gcq#38: "I'm Your Worst Nightmare" (Creep)

-------------------------------------------------------------------------
my enermin.mdp file is .......................
-------------------------------------------------
title               =  sp position restraining
cpp                 =  /usr/bin/cpp
define              =  -DPOSRES
constraints         =  all-bonds
constraint_algorithm=  lincs
lincs_order         =  4
lincs_iter          =  6
lincs_warnangle     =  30
integrator      = steep         ; Algorithm (steep = steepest descent minimization)
dt                  =  0.002    ; ps !
nsteps          = 50000         ; Maximum number of (minimization) steps to perform
nstlog              =  200
nstlist             =  1
ns_type             =  grid
rlist           = 1.2           ; Cut-off for making neighbor list (short range forces)
rcoulomb            =  1.2
rvdw                =  1.2
coulombtype         =  PME
fourierspacing      =  0.12
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order           =  4
ewald_rtol          = 1e-5
optimize_fft        = yes
pbc             = xyz           ; Periodic Boundary Conditions (yes/no)
;
;       Energy minimizing stuff
;
emtol               =  1000
emstep              =  0.01
                      

---------------
should i continue further compression with this energy minimized structure (em_14.gro)??
if not how can i slove this problem.
waiting for ur suggestion.
Moutusi Manna


 
 

 


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