[gmx-users] tcoupling

[shahrbanoo karbalaee]

hi justin
I have a file  tfe  peptide water,cl  .I  minimized it and I  want to
preequilbrate it.when I do the grompp  I get  1 warning:
 calling /lib/cpp...
processing topology...
Generated 165 of the 1596 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein_A 1
turning all bonds into constraints...
Excluding 3 bonded neighbours for TFE 200
turning all bonds into constraints...
Excluding 2 bonded neighbours for SOL 913
turning all bonds into constraints...
Excluding 1 bonded neighbours for CL- 1
turning all bonds into constraints...
NOTE:
  System has non-zero total charge: -1.000003e+00

processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
Reading position restraint coords from emout.gro
renumbering atomtypes...
converting bonded parameters...
#  G96ANGLES:   1803
#      PDIHS:   468
#      IDIHS:   68
#       LJ14:   1010
#     POSRES:   105
#     CONSTR:   1339
#     SETTLE:   913
Walking down the molecule graph to make shake-blocks
initialising group options...
processing index file...
Analysing residue names:
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
There are:  1114      OTHER residues
There are:    14    PROTEIN residues
There are:     0        DNA residues
Analysing Protein...
Analysing Other...
WARNING 1 [file aminoacids.dat, line 1]:
  T-Coupling group Protein has fewer than 10% of the atoms (138 out of
  4278)
  Maybe you want to try Protein and Non-Protein instead?
Making dummy/rest group for Acceleration containing 4278 elements
Making dummy/rest group for Freeze containing 4278 elements
Making dummy/rest group for Energy Mon. containing 4278 elements
Making dummy/rest group for VCM containing 4140 elements
Number of degrees of freedom in T-Coupling group Protein is 272.00
Number of degrees of freedom in T-Coupling group Non-Protein is 8478.00
Making dummy/rest group for User1 containing 4278 elements
Making dummy/rest group for User2 containing 4278 elements
Making dummy/rest group for XTC containing 4278 elements
Making dummy/rest group for Or. Res. Fit containing 4278 elements
Making dummy/rest group for QMMM containing 4278 elements
T-Coupling       has 2 element(s): Protein Non-Protein
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 2 element(s): Protein rest
XTC              has 1 element(s): rest
Or. Res. Fit     has 1 element(s): rest
QMMM             has 1 element(s): rest
Checking consistency between energy and charge groups...
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 50x50x50, spacing 0.120 0.120 0.120
writing run input file...

Back Off! I just backed up prout.tpr to ./#prout.tpr.1#

There was 1 warning

In pr.mdp ,I creat  two group  protein and nonprotein but it is not correct.

cpp                 =  /lib/cpp
define              =  -DPOSRES
constraints         =  all-bonds
comm_grps           = protein
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  2000000    ; total .
nstcomm             =  1
nstxout             =  100
nstvout             =  1000
nstfout             =  0
nstlog              =  100
nstenergy           =  100
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1
coulombtype         =  pme
rvdw                =  1
ewald_rtol          = 1e-5
fourierspacing      =  0.12
; Berendsen temperature coupling is on
Tcoupl              =  berendsen
pcoupltype          =  isotropic
tau_t               =  0.1         0.1
tc-grps             =  Protein    non-protein
ref_t               =  300        300
; Pressure coupling is  no
pcoupl              =  no
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529
please suggest me and advise.
thanks

-- 
sh-karbalaee