[gmx-users] error in "cg" and "steep"

[Alok]

hello
        Thanks Dr. Nuno & Dr. David for your previous help .
      I am trying to simulate four peptide(12 residue 80 atoms) in
methanol solvent(6021 residue 18063 atoms).I am getting error while Energy
Minimization by using "cg"  and getting warning when i am using "steep".
       I am using constrains = none  in .mdp file .
But when i am using "cg" i am getting fatal error  :- can not do Conjugate
Gradients with constraints (18063)
       And when i am using "steep" i am getting warning :-
For minimization with LINCS constraints, lincs_iter should be 4 to 8.

I am sending output from grompp for both "cg" & "steep"



output from grompp when i used "cg":-

checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 432 of the 1378 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein_A 1
Excluding 3 bonded neighbours for Protein_B 1
Excluding 3 bonded neighbours for Protein_C 1
Excluding 3 bonded neighbours for Protein_D 1
Excluding 2 bonded neighbours for Methanol 6021
WARNING 1 [file "gpg.top", line 30]:
  System has non-zero total charge: -1.794398e-04

processing coordinates...
double-checking input for internal consistency...
ERROR: can not do Conjugate Gradients with constraints (18063)
There was 1 warning
Fatal error: There was 1 error




output from grompp when i used "steep":-

reating statusfile for 1 node...
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 432 of the 1378 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein_A 1
Excluding 3 bonded neighbours for Protein_B 1
Excluding 3 bonded neighbours for Protein_C 1
Excluding 3 bonded neighbours for Protein_D 1
Excluding 2 bonded neighbours for Methanol 6021
WARNING 1 [file "gpg.top", line 30]:
  System has non-zero total charge: -1.794398e-04

processing coordinates...
double-checking input for internal consistency...
WARNING 2 [file "gpg.top", line 30]:
  For minimization with LINCS constraints, lincs_iter should be 4 to 8.
renumbering atomtypes...
converting bonded parameters...
#   G96BONDS:   240
#  G96ANGLES:   432
#      PDIHS:   260
#      IDIHS:   120
#       LJ14:   324
#     CONSTR:   54189
Walking down the molecule graph to make shake-blocks
initialising group options...
processing index file...
Analysing residue names:
Opening library file /usr/local/share/gromacs/top/aminoacids.dat
There are:  6021      OTHER residues
There are:    12    PROTEIN residues
There are:     0        DNA residues
Analysing Protein...
Analysing Other...
Making dummy/rest group for T-Coupling containing 18143 elements
Not using any simulated annealing
Making dummy/rest group for Acceleration containing 18143 elements Making
dummy/rest group for Freeze containing 18143 elements
Making dummy/rest group for Energy Mon. containing 18143 elements
Making dummy/rest group for VCM containing 18143 elements
Number of degrees of freedom in T-Coupling group rest is 36363.00
Making dummy/rest group for User1 containing 18143 elements
Making dummy/rest group for User2 containing 18143 elements
Making dummy/rest group for XTC containing 18143 elements
Making dummy/rest group for Or. Res. Fit containing 18143 elements T-Coupling
    has 1 element(s): rest
Energy Mon.      has 1 element(s): rest
Acceleration     has 1 element(s): rest
Freeze           has 1 element(s): rest
User1            has 1 element(s): rest
User2            has 1 element(s): rest
VCM              has 1 element(s): rest
XTC              has 1 element(s): rest
Or. Res. Fit     has 1 element(s): rest
Checking consistency between energy and charge groups...
writing run input file...
There were 2 warnings



I also want to know how one can distinguish between the parametres from
mdout.mdp ,especially the parametres given by my .mdp file and the
parametres specified in mdout.mdp . I am not able to distinguish between
paramters which the programs uses(specified by my .mdp) and the other
parametres which it does not uses in mdout.mdp.

With regards
Alok