[gmx-users] how to set files for free energy caculation?

[zhongjin]

Dear GMX users,
  Recently, I want to caculate the free energy for K+----->NA+ in bulk with GMX4.5.4 using charmm 27 force field.  I change ion.itp
[ moleculetype ]
; molname nrexcl
K  1
[ atoms ]
; id at type    res nr  residu name at name  cg nr   charge   
1 POT        1     K     K      1       1   
 
to
 
[ moleculetype ]
; molname nrexcl
K  1
[ atoms ]
; id at type    res nr  residu name at name  cg nr   charge   mass         typeB    chargeB      massB
1 POT        1     K     K      1       1     39.102000      SOD        1       22.989770 
#ifdef POSRES_K
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1        1000000    1000000     1000000
#endif
 
and include it into .top file.
 
And I set .mdp file
; Free energy control stuff
free-energy              = yes
init-lambda              = 0.0
delta-lambda             = 0
foreign_lambda           = 0.05
sc-alpha                 = 0.5
sc-power                 = 1.0
sc-sigma                 = 0.3
nstdhdl                  = 10
separate-dhdl-file       = yes
dhdl-derivatives         = yes
dh_hist_size             = 0
dh_hist_spacing          = 0.1
couple-moltype           = K
couple-lambda0           = vdw-q
couple-lambda1           = vdw-q
couple-intramol          = no
 
however when I do EM, there are two warnings and stop.
WARNING 1 [file min.mdp, line 329]:
  The lambda=0 and lambda=1 states for coupling are identical
Generated 28 of the 28 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 28 of the 28 1-4 parameter combinations
WARNING 2 [file ion.itp, line 22]:
  Some parameters for bonded interaction involving perturbed atoms are
  specified explicitly in state A, but not B - copying A to B
Excluding 3 bonded neighbours molecule type 'gra'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'K'
Coupling 1 copies of molecule type 'K'
NOTE 1 [file topol.top, line 16]:
  System has non-zero total charge: 1.000000e+00
  

Analysing residue names:
There are:     1      Other residues
There are:   531      Water residues
There are:     1        Ion residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group rest is 3660.00
Largest charge group radii for Van der Waals: 0.040, 0.040 nm
Largest charge group radii for Coulomb:       0.079, 0.079 nm
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 20x20x30, spacing 0.115 0.115 0.115
Estimate for the relative computational load of the PME mesh part: 0.36
This run will generate roughly 22 Mb of data
There was 1 note
There were 2 warnings
-------------------------------------------------------
Program grompp, VERSION 4.5.4
Source code file: grompp.c, line: 1582
Fatal error:
Too many warnings (2), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
"Your Proposal is Accepted" (Men In Black)
 
It seems that 
[ moleculetype ]
; molname nrexcl
K  1
[ atoms ]
; id at type    res nr  residu name at name  cg nr   charge   mass         typeB    chargeB      massB
1 POT        1     K     K      1       1     39.102000      SOD        1       22.989770 
do not take effect.
 
Thanks in advance!
 
Zhongjin He
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