[gmx-users] free energy

Nilesh Dhumal ndhumal at andrew.cmu.edu
Sun Jan 3 18:24:06 CET 2010


Hey All,
I am trying to calculate the solvation free energy of glucose in ionic
liquids. I am getting really large  value for lamda=0 in vacuum and
solvent as well. I am getting final solvation energy value ~ 310 kJ/mol.
Can you tell me where I am   wrong.
Here I have pasted the the lamda value in vacuum and  solvent

Vacuum 		 Solvent

0.0 527.16	0.0 4284.769
0.1 74.119	0.1 161.606
0.2 37.9665	0.2 -16.3176
0.3 28.748	0.3 -52.488
0.4 7.555	0.4 -4.3341
0.5 1.495	0.5 6.996
0.6 -4.796	0.6 155.485
0.7 2.361	0.7 174.20
0.8 3.69	0.8 193.016
0.9 5.483	0.9  201.820
0.92 6.391	0.92 211.79
1.0 8.887	1.0  227.79

For each lamda value I equibrate the system for 1ns and run the dynamics
for 4 ns.
here is dynamics file I used. pasted the topology file at the end.


title               =  cpeptide MD
cpp                 =  /usr/bin/cpp
constraints         =  none
integrator          =  md
dt                  =  0.001    ; ps !
nsteps              =  4000000     ; total 5 ps.
nstcomm             =  1
nstxout             =  50
nstvout             =  0
nstfout             =  0
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.4
coulombtype         = PME
vdwtype             = cut-off
pbc                 = xyz
fourierspacing      = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order           = 4
ewald_rtol          = 1e-5
optimize_fft        = yes
; Berendsen temperature coupling is on
Tcoupl = v-rescale
tau_t = 0.1
tc-grps  =system
ref_t =   350
; Pressure coupling is  on
Pcoupl              = parrinello-rahman
pcoupltype          = isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  350.0
gen_seed            =  173529
free_energy         = yes
init_lambda         = 0.00
sc-alpha            = 0.6
sc_power            = 1


Thanks

Nilesh


Topology file (not pasted whole because of size)
;
;	File 'glu-ac.top' was generated
;	By user: ndhumal (36026)
;	On host: c20
;	At date: Tue Dec 15 15:25:07 2009
;
;	This is your topology file
;	Gromacs Runs One Microsecond At Cannonball Speeds
;
; Include forcefield parameters
#include "ffoplsaa.itp"

[ moleculetype ]
; Name            nrexcl
Protein             3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
   chargeB      massB
     1   opls_180      1    GUL      O      1       -0.4    15.9994  
opls_180  0.0    15.9994
     2   opls_159      1    GUL     C2      2      0.365     12.011  
opls_159  0.0     12.011
     3   opls_159      1    GUL     C3      2      0.205     12.011  
opls_159  0.0     12.011
     4   opls_159      1    GUL     C4      2      0.205     12.011  
opls_159  0.0     12.011
     5   opls_159      1    GUL     C5      2      0.205     12.011  
opls_159  0.0     12.011
     6   opls_137      1    GUL     C6      2       0.17     12.011  
opls_137  0.0     12.011
     7   opls_159      1    GUL     C7      2      0.145     12.011  
opls_159  0.0     12.011
     8   opls_169      1    GUL     O8      3       -0.7    15.9994  
opls_169  0.0    15.9994
     9   opls_169      1    GUL     O9      3       -0.7    15.9994  
opls_169  0.0    15.9994
    10   opls_169      1    GUL    O10      3       -0.7    15.9994  
opls_169  0.0    15.9994
    11   opls_169      1    GUL    O11      3       -0.7    15.9994  
opls_169  0.0    15.9994
    12   opls_154      1    GUL    O12      3     -0.683    15.9994  
opls_154  0.0    15.9994
    13   opls_140      1    GUL    H13      4        0.1      1.008  
opls_140  0.0      1.008
    14   opls_140      1    GUL    H14      4       0.06      1.008  
opls_140  0.0      1.008
    15   opls_140      1    GUL    H15      4       0.06      1.008  
opls_140  0.0      1.008
    16   opls_140      1    GUL    H16      4       0.06      1.008  
opls_140  0.0      1.008
    17   opls_140      1    GUL    H17      4       0.03      1.008  
opls_140  0.0      1.008
    18   opls_155      1    GUL    H18      5      0.435      1.008  
opls_155  0.0      1.008
    19   opls_155      1    GUL    H19      5      0.435      1.008  
opls_155  0.0      1.008
    20   opls_155      1    GUL    H20      5      0.435      1.008  
opls_155  0.0      1.008
    21   opls_155      1    GUL    H21      5      0.435      1.008  
opls_155  0.0      1.008
    22   opls_140      1    GUL    H22      5       0.06      1.008  
opls_140  0.0      1.008
    23   opls_140      1    GUL    H23      5       0.06      1.008  
opls_140  0.0      1.008
    24   opls_155      1    GUL    H24      6      0.418      1.008  
opls_155  0.0      1.008
    25   opls_561      2    EMI      C      7      -0.13     12.011   ;
qtot -0.13
    26   opls_561      2    EMI     C2      8      -0.13     12.011   ;
qtot -0.26
    27   opls_557      2    EMI     N3      9       0.15    14.0067   ;
qtot -0.11
    28   opls_558      2    EMI     C4     10      -0.11     12.011   ;
qtot -0.22
    29   opls_557      2    EMI     N5     11       0.15    14.0067   ;
qtot -0.07
    30   opls_135      2    EMI     C6     12      -0.17     12.011   ;
qtot -0.24
    31   opls_136      2    EMI     C7     13      -0.05     12.011   ;
qtot -0.29
    32   opls_135      2    EMI     C8     14      -0.17     12.011   ;
qtot -0.46
    33   opls_564      2    EMI     H9     15       0.21      1.008   ;
qtot -0.25
    34   opls_564      2    EMI    H10     15       0.21      1.008   ;
qtot -0.04
    35   opls_563      2    EMI    H11     15       0.21      1.008   ;
qtot 0.17
    36   opls_140      2    EMI    H12     16       0.13      1.008   ;
qtot 0.3
    37   opls_140      2    EMI    H13     16       0.13      1.008   ;
qtot 0.43
    38   opls_140      2    EMI    H14     16       0.13      1.008   ;
qtot 0.56
    39   opls_140      2    EMI    H15     17       0.13      1.008   ;
qtot 0.69
    40   opls_140      2    EMI    H16     17       0.13      1.008   ;
qtot 0.82
    41   opls_140      2    EMI    H17     18       0.06      1.008   ;
qtot 0.88
    42   opls_140      2    EMI    H18     18       0.06      1.008   ;
qtot 0.94
    43   opls_140      2    EMI    H19     18       0.06      1.008   ;
qtot 1
    44   opls_561      3    EMI      C     19      -0.13     12.011   ;
qtot 0.87
    45   opls_561      3    EMI     C2     20      -0.13     12.011   ;
qtot 0.74
    46   opls_557      3    EMI     N3     21       0.15    14.0067   ;
qtot 0.89
    47   opls_558      3    EMI     C4     22      -0.11     12.011   ;
qtot 0.78
    48   opls_557      3    EMI     N5     23       0.15    14.0067   ;
qtot 0.93
    49   opls_135      3    EMI     C6     24      -0.17     12.011   ;
qtot 0.76
    50   opls_136      3    EMI     C7     25      -0.05     12.011   ;
qtot 0.71
    51   opls_135      3    EMI     C8     26      -0.17     12.011   ;
qtot 0.54
    52   opls_564      3    EMI     H9     27       0.21      1.008   ;
qtot 0.75
    53   opls_564      3    EMI    H10     27       0.21      1.008   ;
qtot 0.96
    54   opls_563      3    EMI    H11     27       0.21      1.008   ;
qtot 1.17
    55   opls_140      3    EMI    H12     28       0.13      1.008   ;
qtot 1.3
    56   opls_140      3    EMI    H13     28       0.13      1.008   ;
qtot 1.43
    57   opls_140      3    EMI    H14     28       0.13      1.008   ;
qtot 1.56
    58   opls_140      3    EMI    H15     29       0.13      1.008   ;
qtot 1.69
    59   opls_140      3    EMI    H16     29       0.13      1.008   ;
qtot 1.82
    60   opls_140      3    EMI    H17     30       0.06      1.008   ;
qtot 1.88
    61   opls_140      3    EMI    H18     30       0.06      1.008   ;
qtot 1.94
    62   opls_140      3    EMI    H19     30       0.06      1.008   ;
qtot 2
    63   opls_561      4    EMI      C     31      -0.13     12.011   ;
qtot 1.87
    64   opls_561      4    EMI     C2     32      -0.13     12.011   ;
qtot 1.74
    65   opls_557      4    EMI     N3     33       0.15    14.0067   ;
qtot 1.89
    66   opls_558      4    EMI     C4     34      -0.11     12.011   ;
qtot 1.78
    67   opls_557      4    EMI     N5     35       0.15    14.0067   ;
qtot 1.93
    68   opls_135      4    EMI     C6     36      -0.17     12.011   ;
qtot 1.76
    69   opls_136      4    EMI     C7     37      -0.05     12.011   ;
qtot 1.71
    70   opls_135      4    EMI     C8     38      -0.17     12.011   ;
qtot 1.54
    71   opls_564      4    EMI     H9     39       0.21      1.008   ;
qtot 1.75
    72   opls_564      4    EMI    H10     39       0.21      1.008   ;
qtot 1.96
    73   opls_563      4    EMI    H11     39       0.21      1.008   ;
qtot 2.17
    74   opls_140      4    EMI    H12     40       0.13      1.008   ;
qtot 2.3
    75   opls_140      4    EMI    H13     40       0.13      1.008   ;
qtot 2.43
    76   opls_140      4    EMI    H14     40       0.13      1.008   ;
qtot 2.56
    77   opls_140      4    EMI    H15     41       0.13      1.008   ;
qtot 2.69
    78   opls_140      4    EMI    H16     41       0.13      1.008   ;
qtot 2.82
    79   opls_140      4    EMI    H17     42       0.06      1.008   ;
qtot 2.88
    80   opls_140      4    EMI    H18     42       0.06      1.008   ;
qtot 2.94
    81   opls_140      4    EMI    H19     42       0.06      1.008   ;
qtot 3
    82   opls_561      5    EMI      C     43      -0.13     12.011   ;
qtot 2.87
    83   opls_561      5    EMI     C2     44      -0.13     12.011   ;
qtot 2.74
    84   opls_557      5    EMI     N3     45       0.15    14.0067   ;
qtot 2.89
    85   opls_558      5    EMI     C4     46      -0.11     12.011   ;
qtot 2.78
    86   opls_557      5    EMI     N5     47       0.15    14.0067   ;
qtot 2.93
    87   opls_135      5    EMI     C6     48      -0.17     12.011   ;
qtot 2.76
    88   opls_136      5    EMI     C7     49      -0.05     12.011   ;
qtot 2.71
    89   opls_135      5    EMI     C8     50      -0.17     12.011   ;
qtot 2.54
    90   opls_564      5    EMI     H9     51       0.21      1.008   ;
qtot 2.75
    91   opls_564      5    EMI    H10     51       0.21      1.008   ;
qtot 2.96
    92   opls_563      5    EMI    H11     51       0.21      1.008   ;
qtot 3.17
    93   opls_140      5    EMI    H12     52       0.13      1.008   ;
qtot 3.3
    94   opls_140      5    EMI    H13     52       0.13      1.008   ;
qtot 3.43
    95   opls_140      5    EMI    H14     52       0.13      1.008   ;
qtot 3.56
    96   opls_140      5    EMI    H15     53       0.13      1.008   ;
qtot 3.69
    97   opls_140      5    EMI    H16     53       0.13      1.008   ;
qtot 3.82
    98   opls_140      5    EMI    H17     54       0.06      1.008   ;
qtot 3.88
    99   opls_140      5    EMI    H18     54       0.06      1.008   ;
qtot 3.94
   100   opls_140      5    EMI    H19     54       0.06      1.008   ;
qtot 4
   101   opls_561      6    EMI      C     55      -0.13     12.011   ;
qtot 3.87
   102   opls_561      6    EMI     C2     56      -0.13     12.011   ;
qtot 3.74
   103   opls_557      6    EMI     N3     57       0.15    14.0067   ;
qtot 3.89
   104   opls_558      6    EMI     C4     58      -0.11     12.011   ;
qtot 3.78
   105   opls_557      6    EMI     N5     59       0.15    14.0067   ;
qtot 3.93
   106   opls_135      6    EMI     C6     60      -0.17     12.011   ;
qtot 3.76
   107   opls_136      6    EMI     C7     61      -0.05     12.011   ;
qtot 3.71
   108   opls_135      6    EMI     C8     62      -0.17     12.011   ;
qtot 3.54
   109   opls_564      6    EMI     H9     63       0.21      1.008   ;
qtot 3.75
   110   opls_564      6    EMI    H10     63       0.21      1.008   ;
qtot 3.96
   111   opls_563      6    EMI    H11     63       0.21      1.008   ;
qtot 4.17
   112   opls_140      6    EMI    H12     64       0.13      1.008   ;
qtot 4.3
   113   opls_140      6    EMI    H13     64       0.13      1.008   ;
qtot 4.43
   114   opls_140      6    EMI    H14     64       0.13      1.008   ;
qtot 4.56
   115   opls_140      6    EMI    H15     65       0.13      1.008   ;
qtot 4.69
   116   opls_140      6    EMI    H16     65       0.13      1.008   ;
qtot 4.82
   117   opls_140      6    EMI    H17     66       0.06      1.008   ;
qtot 4.88
   118   opls_140      6    EMI    H18     66       0.06      1.008   ;
qtot 4.94
   119   opls_140      6    EMI    H19     66       0.06      1.008   ;
qtot 5
   120   opls_561      7    EMI      C     67      -0.13     12.011   ;
qtot 4.87
   121   opls_561      7    EMI     C2     68      -0.13     12.011   ;
qtot 4.74
   122   opls_557      7    EMI     N3     69       0.15    14.0067   ;
qtot 4.89
   123   opls_558      7    EMI     C4     70      -0.11     12.011   ;
qtot 4.78
   124   opls_557      7    EMI     N5     71       0.15    14.0067   ;
qtot 4.93
   125   opls_135      7    EMI     C6     72      -0.17     12.011   ;
qtot 4.76
   126   opls_136      7    EMI     C7     73      -0.05     12.011   ;
qtot 4.71
   127   opls_135      7    EMI     C8     74      -0.17     12.011   ;
qtot 4.54
   128   opls_564      7    EMI     H9     75       0.21      1.008   ;
qtot 4.75
   129   opls_564      7    EMI    H10     75       0.21      1.008   ;
qtot 4.96
   130   opls_563      7    EMI    H11     75       0.21      1.008   ;
qtot 5.17
   131   opls_140      7    EMI    H12     76       0.13      1.008   ;
qtot 5.3
   132   opls_140      7    EMI    H13     76       0.13      1.008   ;
qtot 5.43
   133   opls_140      7    EMI    H14     76       0.13      1.008   ;
qtot 5.56
   134   opls_140      7    EMI    H15     77       0.13      1.008   ;
qtot 5.69
   135   opls_140      7    EMI    H16     77       0.13      1.008   ;
qtot 5.82
   136   opls_140      7    EMI    H17     78       0.06      1.008   ;
qtot 5.88
   137   opls_140      7    EMI    H18     78       0.06      1.008   ;
qtot 5.94
   138   opls_140      7    EMI    H19     78       0.06      1.008   ;
qtot 6
   139   opls_561      8    EMI      C     79      -0.13     12.011   ;
qtot 5.87
   140   opls_561      8    EMI     C2     80      -0.13     12.011   ;
qtot 5.74
   141   opls_557      8    EMI     N3     81       0.15    14.0067   ;
qtot 5.89
   142   opls_558      8    EMI     C4     82      -0.11     12.011   ;
qtot 5.78
   143   opls_557      8    EMI     N5     83       0.15    14.0067   ;
qtot 5.93
   144   opls_135      8    EMI     C6     84      -0.17     12.011   ;
qtot 5.76
   145   opls_136      8    EMI     C7     85      -0.05     12.011   ;
qtot 5.71
   146   opls_135      8    EMI     C8     86      -0.17     12.011   ;
qtot 5.54
   147   opls_564      8    EMI     H9     87       0.21      1.008   ;
qtot 5.75
   148   opls_564      8    EMI    H10     87       0.21      1.008   ;
qtot 5.96
   149   opls_563      8    EMI    H11     87       0.21      1.008   ;
qtot 6.17
   150   opls_140      8    EMI    H12     88       0.13      1.008   ;
qtot 6.3
   151   opls_140      8    EMI    H13     88       0.13      1.008   ;
qtot 6.43
   152   opls_140      8    EMI    H14     88       0.13      1.008   ;
qtot 6.56
   153   opls_140      8    EMI    H15     89       0.13      1.008   ;
qtot 6.69
   154   opls_140      8    EMI    H16     89       0.13      1.008   ;
qtot 6.82
   155   opls_140      8    EMI    H17     90       0.06      1.008   ;
qtot 6.88
   156   opls_140      8    EMI    H18     90       0.06      1.008   ;
qtot 6.94
   157   opls_140      8    EMI    H19     90       0.06      1.008   ;
qtot 7
   158   opls_561      9    EMI      C     91      -0.13     12.011   ;
qtot 6.87
   159   opls_561      9    EMI     C2     92      -0.13     12.011   ;
qtot 6.74
   160   opls_557      9    EMI     N3     93       0.15    14.0067   ;
qtot 6.89
   161   opls_558      9    EMI     C4     94      -0.11     12.011   ;
qtot 6.78
   162   opls_557      9    EMI     N5     95       0.15    14.0067   ;
qtot 6.93
   163   opls_135      9    EMI     C6     96      -0.17     12.011   ;
qtot 6.76
   164   opls_136      9    EMI     C7     97      -0.05     12.011   ;
qtot 6.71
   165   opls_135      9    EMI     C8     98      -0.17     12.011   ;
qtot 6.54
   166   opls_564      9    EMI     H9     99       0.21      1.008   ;
qtot 6.75
   167   opls_564      9    EMI    H10     99       0.21      1.008   ;
qtot 6.96
   168   opls_563      9    EMI    H11     99       0.21      1.008   ;
qtot 7.17
   169   opls_140      9    EMI    H12    100       0.13      1.008   ;
qtot 7.3
   170   opls_140      9    EMI    H13    100       0.13      1.008   ;
qtot 7.43
   171   opls_140      9    EMI    H14    100       0.13      1.008   ;
qtot 7.56
   172   opls_140      9    EMI    H15    101       0.13      1.008   ;
qtot 7.69
   173   opls_140      9    EMI    H16    101       0.13      1.008   ;
qtot 7.82
   174   opls_140      9    EMI    H17    102       0.06      1.008   ;
qtot 7.88
   175   opls_140      9    EMI    H18    102       0.06      1.008   ;
qtot 7.94
   176   opls_140      9    EMI    H19    102       0.06      1.008   ;
qtot 8
   177   opls_561     10    EMI      C    103      -0.13     12.011   ;
qtot 7.87
   178   opls_561     10    EMI     C2    104      -0.13     12.011   ;
qtot 7.74
   179   opls_557     10    EMI     N3    105       0.15    14.0067   ;
qtot 7.89
   180   opls_558     10    EMI     C4    106      -0.11     12.011   ;
qtot 7.78
   181   opls_557     10    EMI     N5    107       0.15    14.0067   ;
qtot 7.93
   182   opls_135     10    EMI     C6    108      -0.17     12.011   ;
qtot 7.76
   183   opls_136     10    EMI     C7    109      -0.05     12.011   ;
qtot 7.71
   184   opls_135     10    EMI     C8    110      -0.17     12.011   ;
qtot 7.54
   185   opls_564     10    EMI     H9    111       0.21      1.008   ;
qtot 7.75
   186   opls_564     10    EMI    H10    111       0.21      1.008   ;
qtot 7.96
   187   opls_563     10    EMI    H11    111       0.21      1.008   ;
qtot 8.17
   188   opls_140     10    EMI    H12    112       0.13      1.008   ;
qtot 8.3
   189   opls_140     10    EMI    H13    112       0.13      1.008   ;
qtot 8.43
   190   opls_140     10    EMI    H14    112       0.13      1.008   ;
qtot 8.56
   191   opls_140     10    EMI    H15    113       0.13      1.008   ;
qtot 8.69
   192   opls_140     10    EMI    H16    113       0.13      1.008   ;
qtot 8.82
   193   opls_140     10    EMI    H17    114       0.06      1.008   ;
qtot 8.88
   194   opls_140     10    EMI    H18    114       0.06      1.008   ;
qtot 8.94
   195   opls_140     10    EMI    H19    114       0.06      1.008   ;
qtot 9
   196   opls_561     11    EMI      C    115      -0.13     12.011   ;
qtot 8.87
   197   opls_561     11    EMI     C2    116      -0.13     12.011   ;
qtot 8.74
   198   opls_557     11    EMI     N3    117       0.15    14.0067   ;
qtot 8.89
   199   opls_558     11    EMI     C4    118      -0.11     12.011   ;
qtot 8.78
   200   opls_557     11    EMI     N5    119       0.15    14.0067   ;
qtot 8.93
   201   opls_135     11    EMI     C6    120      -0.17     12.011   ;
qtot 8.76
   202   opls_136     11    EMI     C7    121      -0.05     12.011   ;
qtot 8.71
   203   opls_135     11    EMI     C8    122      -0.17     12.011   ;
qtot 8.54
   204   opls_564     11    EMI     H9    123       0.21      1.008   ;
qtot 8.75
   205   opls_564     11    EMI    H10    123       0.21      1.008   ;
qtot 8.96
   206   opls_563     11    EMI    H11    123       0.21      1.008   ;
qtot 9.17
   207   opls_140     11    EMI    H12    124       0.13      1.008   ;
qtot 9.3
   208   opls_140     11    EMI    H13    124       0.13      1.008   ;
qtot 9.43
   209   opls_140     11    EMI    H14    124       0.13      1.008   ;
qtot 9.56
   210   opls_140     11    EMI    H15    125       0.13      1.008   ;
qtot 9.69
   211   opls_140     11    EMI    H16    125       0.13      1.008   ;
qtot 9.82
   212   opls_140     11    EMI    H17    126       0.06      1.008   ;
qtot 9.88
   213   opls_140     11    EMI    H18    126       0.06      1.008   ;
qtot 9.94
   214   opls_140     11    EMI    H19    126       0.06      1.008   ;
qtot 10
   215   opls_561     12    EMI      C    127      -0.13     12.011   ;
qtot 9.87
   216   opls_561     12    EMI     C2    128      -0.13     12.011   ;
qtot 9.74
   217   opls_557     12    EMI     N3    129       0.15    14.0067   ;
qtot 9.89
   218   opls_558     12    EMI     C4    130      -0.11     12.011   ;
qtot 9.78
   219   opls_557     12    EMI     N5    131       0.15    14.0067   ;
qtot 9.93
   220   opls_135     12    EMI     C6    132      -0.17     12.011   ;
qtot 9.76
   221   opls_136     12    EMI     C7    133      -0.05     12.011   ;
qtot 9.71
   222   opls_135     12    EMI     C8    134      -0.17     12.011   ;
qtot 9.54
   223   opls_564     12    EMI     H9    135       0.21      1.008   ;
qtot 9.75
   224   opls_564     12    EMI    H10    135       0.21      1.008   ;
qtot 9.96
   225   opls_563     12    EMI    H11    135       0.21      1.008   ;
qtot 10.17
   226   opls_140     12    EMI    H12    136       0.13      1.008   ;
qtot 10.3
   227   opls_140     12    EMI    H13    136       0.13      1.008   ;
qtot 10.43
   228   opls_140     12    EMI    H14    136       0.13      1.008   ;
qtot 10.56
   229   opls_140     12    EMI    H15    137       0.13      1.008   ;
qtot 10.69
   230   opls_140     12    EMI    H16    137       0.13      1.008   ;
qtot 10.82
   231   opls_140     12    EMI    H17    138       0.06      1.008   ;
qtot 10.88
   232   opls_140     12    EMI    H18    138       0.06      1.008   ;
qtot 10.94
   233   opls_140     12    EMI    H19    138       0.06      1.008   ;
qtot 11




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