[gmx-users] gromacs.org_gmx-users Digest, Vol 142, Issue 1

Mehreen Jan mehreen_jan1990 at yahoo.com
Mon Feb 1 07:04:14 CET 2016


how to run gromacs for protein protein interaction having phosphorylated at SER and THR.
error:
residue TPO not found in residue topology database
modification are done from the given web.
http://www.gromacs.org/Downloads/User_contributions/Force_fields

>make changes in .rtp file
make changes in .dat file
forcefield 43A1 is used.

command:
pdb2gmx -f protein.pdb -p protein.top -o protein.gro
error:
residue "TPO" not found in residue topology database

make changes in residuestypes.dat
fallowing are the changes make in .rtp file

; [ SEP ] [ TPO ] [ PTR ] -PO4^{-2} forms
; [ SEPH ] [ TPOH ] [ PTRH ] -PO4H^{-1} forms


[ SEP ]
[ atoms ]
    N     N    -0.28000     0
    H     H     0.28000     0
   CA   CH1     0.00000     1
   CB   CH2     0.00000     2
   OG    OA    -0.36000     2
    P     P     0.94000     2
  O1P    OP    -0.86000     2
  O2P    OP    -0.86000     2
  O3P    OP    -0.86000     2
    C     C       0.380     3
    O     O      -0.380     3
[ bonds ]
    N     H    gb_2   
    N    CA    gb_20   
   CA     C    gb_26   
    C     O    gb_4   
    C    +N    gb_9   
   CA    CB    gb_26   
   CB    OG    gb_17   
   OG     P    gb_27   
    P   O1P    gb_23   
    P   O2P    gb_23   
    P   O3P    gb_23   
[ angles ]
;  ai    aj    ak   gromos type
   -C     N     H     ga_31   
    H     N    CA     ga_17   
   -C     N    CA     ga_30   
    N    CA     C     ga_12   
   CA     C    +N     ga_18   
   CA     C     O     ga_29   
    O     C    +N     ga_32   
    N    CA    CB     ga_12   
    C    CA    CB     ga_12   
   CA    CB    OG     ga_12   
   CB    OG     P     ga_25
   OG     P   O1P     ga_13
   OG     P   O2P     ga_13
   OG     P   O3P     ga_13
  O1P     P   O2P     ga_28
  O1P     P   O3P     ga_28
  O2P     P   O3P     ga_28
[ impropers ]
;  ai    aj    ak    al   gromos type
    N    -C    CA     H     gi_1   
    C    CA    +N     O     gi_1   
   CA     N     C    CB     gi_2   
[ dihedrals ]
;  ai    aj    ak    al   gromos type
  -CA    -C     N    CA     gd_4   
   -C     N    CA     C     gd_19   
    N    CA     C    +N     gd_20   
    N    CA    CB    OG     gd_17   
   CA    CB    OG     P     gd_14   
   CB    OG     P   O1P     gd_11

[ TPO ]
[ atoms ]
    N     N    -0.28000     0
    H     H     0.28000     0
   CA   CH1     0.00000     1
   CB   CH1     0.00000     2
  OG1    OA    -0.36000     2
    P     P     0.94000     2
  O1P    OP    -0.86000     2
  O2P    OP    -0.86000     2
  O3P    OP    -0.86000     2
  CG2   CH3     0.00000     3
    C     C       0.380     4
    O     O      -0.380     4
[ bonds ]
    N     H    gb_2   
    N    CA    gb_20   
   CA     C    gb_26   
    C     O    gb_4   
    C    +N    gb_9   
   CA    CB    gb_26   
   CB   OG1    gb_17   
   CB   CG2    gb_26   
  OG1     P    gb_27   
    P   O1P    gb_23   
    P   O2P    gb_23   
    P   O3P    gb_23   
[ angles ]
;  ai    aj    ak   gromos type
   -C     N     H     ga_31   
    H     N    CA     ga_17   
   -C     N    CA     ga_30   
    N    CA     C     ga_12   
   CA     C    +N     ga_18   
   CA     C     O     ga_29   
    O     C    +N     ga_32   
    N    CA    CB     ga_12   
    C    CA    CB     ga_12   
   CA    CB   OG1     ga_12   
   CA    CB   CG2     ga_14   
  OG1    CB   CG2     ga_14   
   CB   OG1     P     ga_25
  OG1     P   O1P     ga_13
  OG1     P   O2P     ga_13
  OG1     P   O3P     ga_13
  O1P     P   O2P     ga_28
  O1P     P   O3P     ga_28
  O2P     P   O3P     ga_28
[ impropers ]
;  ai    aj    ak    al   gromos type
    N    -C    CA     H     gi_1   
    C    CA    +N     O     gi_1   
   CA     N     C    CB     gi_2   
   CB   OG1   CG2    CA     gi_2   
[ dihedrals ]
;  ai    aj    ak    al   gromos type
  -CA    -C     N    CA     gd_4   
   -C     N    CA     C     gd_19   
    N    CA     C    +N     gd_20   
    N    CA    CB   OG1     gd_17   
   CA    CB   OG1     P     gd_14   
   CB   OG1     P   O1P     gd_11

[ PTR ]
[ atoms ]
    N     N    -0.28000     0
    H     H     0.28000     0
   CA   CH1     0.00000     1
   CB   CH2     0.00000     1
   CG     C     0.00000     1
  CD1     C    -0.10000     2
  HD1    HC     0.10000     2
  CD2     C    -0.10000     3
  HD2    HC     0.10000     3
  CE1     C    -0.10000     4
  HE1    HC     0.10000     4
  CE2     C    -0.10000     5
  HE2    HC     0.10000     5
   CZ     C     0.00000     6
   OH    OA    -0.36000     6
    P     P     0.94000     6
  O1P    OP    -0.86000     6
  O2P    OP    -0.86000     6
  O3P    OP    -0.86000     6
    C     C       0.380     7
    O     O      -0.380     7
[ bonds ]
    N     H    gb_2   
    N    CA    gb_20   
   CA     C    gb_26   
    C     O    gb_4   
    C    +N    gb_9   
   CA    CB    gb_26   
   CB    CG    gb_26   
   CG   CD1    gb_15   
   CG   CD2    gb_15   
  CD1   HD1    gb_3   
  CD1   CE1    gb_15   
  CD2   HD2    gb_3   
  CD2   CE2    gb_15   
  CE1   HE1    gb_3   
  CE1    CZ    gb_15   
  CE2   HE2    gb_3   
  CE2    CZ    gb_15   
   CZ    OH    gb_12   
   OH     P    gb_27   
    P   O1P    gb_23   
    P   O2P    gb_23   
    P   O3P    gb_23   
[ exclusions ]
;  ai    aj
   CB   HD1
   CB   HD2
   CB   CE1
   CB   CE2
   CG   HE1
   CG   HE2
   CG    CZ
  CD1   HD2
  CD1   CE2
  CD1    OH
  HD1   CD2
  HD1   HE1
  HD1    CZ
  CD2   CE1
  CD2    OH
  HD2   HE2
  HD2    CZ
  CE1   HE2
  HE1   CE2
  HE1    OH
  HE2    OH
[ angles ]
;  ai    aj    ak   gromos type
   -C     N     H     ga_31   
    H     N    CA     ga_17   
   -C     N    CA     ga_30   
    N    CA     C     ga_12   
   CA     C    +N     ga_18   
   CA     C     O     ga_29   
    O     C    +N     ga_32   
    N    CA    CB     ga_12   
    C    CA    CB     ga_12   
   CA    CB    CG     ga_14   
   CB    CG   CD1     ga_26   
   CB    CG   CD2     ga_26   
  CD1    CG   CD2     ga_26   
   CG   CD1   HD1     ga_24   
  HD1   CD1   CE1     ga_24   
   CG   CD1   CE1     ga_26   
   CG   CD2   HD2     ga_24   
  HD2   CD2   CE2     ga_24   
   CG   CD2   CE2     ga_26   
  CD1   CE1   HE1     ga_24   
  HE1   CE1    CZ     ga_24   
  CD1   CE1    CZ     ga_26   
  CD2   CE2   HE2     ga_24   
  HE2   CE2    CZ     ga_24   
  CD2   CE2    CZ     ga_26   
  CE1    CZ   CE2     ga_26   
  CE1    CZ    OH     ga_26   
  CE2    CZ    OH     ga_26   
   CZ    OH     P     ga_25
   OH     P   O1P     ga_13
   OH     P   O2P     ga_13
   OH     P   O3P     ga_13
  O1P     P   O2P     ga_28
  O1P     P   O3P     ga_28
  O2P     P   O3P     ga_28
[ impropers ]
;  ai    aj    ak    al   gromos type
    N    -C    CA     H     gi_1   
    C    CA    +N     O     gi_1   
   CA     N     C    CB     gi_2   
   CG   CD1   CD2    CB     gi_1   
  CD2    CG   CD1   CE1     gi_1   
  CD1    CG   CD2   CE2     gi_1   
   CG   CD1   CE1    CZ     gi_1   
   CG   CD2   CE2    CZ     gi_1   
  CD1   CE1    CZ   CE2     gi_1   
  CD2   CE2    CZ   CE1     gi_1   
  CD1    CG   CE1   HD1     gi_1   
  CD2    CG   CE2   HD2     gi_1   
  CE1    CZ   CD1   HE1     gi_1   
  CE2    CZ   CD2   HE2     gi_1   
   CZ   CE1   CE2    OH     gi_1   
[ dihedrals ]
;  ai    aj    ak    al   gromos type
  -CA    -C     N    CA     gd_4   
   -C     N    CA     C     gd_19   
    N    CA     C    +N     gd_20   
    N    CA    CB    CG     gd_17   
   CA    CB    CG   CD1     gd_20   
  CE1    CZ    OH     P     gd_14   
   CZ    OH     P   O1P     gd_11

; end


[ SEPH ]
[ atoms ]
    N     N    -0.28000     0
    H     H     0.28000     0
   CA   CH1     0.00000     1
   CB   CH2     0.00000     2
   OG    OA    -0.36000     2
    P     P     1.23000     2
  O1P    OP    -0.86000     2
  O2P    OP    -0.86000     2
  O3P    OA    -0.54800     2
  H3P     H     0.39800     2
    C     C       0.380     3
    O     O      -0.380     3
[ bonds ]
    N     H    gb_2   
    N    CA    gb_20   
   CA     C    gb_26   
    C     O    gb_4   
    C    +N    gb_9   
   CA    CB    gb_26   
   CB    OG    gb_17   
   OG     P    gb_27   
    P   O1P    gb_23   
    P   O2P    gb_23   
    P   O3P    gb_23   
  O3P   H3P    gb_1
[ angles ]
;  ai    aj    ak   gromos type
   -C     N     H     ga_31   
    H     N    CA     ga_17   
   -C     N    CA     ga_30   
    N    CA     C     ga_12   
   CA     C    +N     ga_18   
   CA     C     O     ga_29   
    O     C    +N     ga_32   
    N    CA    CB     ga_12   
    C    CA    CB     ga_12   
   CA    CB    OG     ga_12   
   CB    OG     P     ga_25
   OG     P   O1P     ga_13
   OG     P   O2P     ga_13
   OG     P   O3P     ga_4
  O1P     P   O2P     ga_28
  O1P     P   O3P     ga_13
  O2P     P   O3P     ga_13
    P   O3P   H3P     ga_11
[ impropers ]
;  ai    aj    ak    al   gromos type
    N    -C    CA     H     gi_1   
    C    CA    +N     O     gi_1   
   CA     N     C    CB     gi_2   
[ dihedrals ]
;  ai    aj    ak    al   gromos type
  -CA    -C     N    CA     gd_4   
   -C     N    CA     C     gd_19   
    N    CA     C    +N     gd_20   
    N    CA    CB    OG     gd_17   
   CA    CB    OG     P     gd_14   
   CB    OG     P   O1P     gd_11
   OG     P   O3P   H3P     gd_11
[ TPOH ]
[ atoms ]
    N     N    -0.28000     0
    H     H     0.28000     0
   CA   CH1     0.00000     1
   CB   CH1     0.00000     2
  OG1    OA    -0.36000     2
    P     P     1.23000     2
  O1P    OP    -0.86000     2
  O2P    OP    -0.86000     2
  O3P    OA    -0.54800     2
  H3P     H     0.39800     2
  CG2   CH3     0.00000     3
    C     C       0.380     4
    O     O      -0.380     4
[ bonds ]
    N     H    gb_2   
    N    CA    gb_20   
   CA     C    gb_26   
    C     O    gb_4   
    C    +N    gb_9   
   CA    CB    gb_26   
   CB   OG1    gb_17   
   CB   CG2    gb_26   
  OG1     P    gb_27   
    P   O1P    gb_23   
    P   O2P    gb_23   
    P   O3P    gb_23   
  O3P   H3P    gb_1
[ angles ]
;  ai    aj    ak   gromos type
   -C     N     H     ga_31   
    H     N    CA     ga_17   
   -C     N    CA     ga_30   
    N    CA     C     ga_12   
   CA     C    +N     ga_18   
   CA     C     O     ga_29   
    O     C    +N     ga_32   
    N    CA    CB     ga_12   
    C    CA    CB     ga_12   
   CA    CB   OG1     ga_12   
   CA    CB   CG2     ga_14   
  OG1    CB   CG2     ga_14   
   CB   OG1     P     ga_25
  OG1     P   O1P     ga_13
  OG1     P   O2P     ga_13
  OG1     P   O3P     ga_4
  O1P     P   O2P     ga_28
  O1P     P   O3P     ga_13
  O2P     P   O3P     ga_13
    P   O3P   H3P     ga_11
[ impropers ]
;  ai    aj    ak    al   gromos type
    N    -C    CA     H     gi_1   
    C    CA    +N     O     gi_1   
   CA     N     C    CB     gi_2   
   CB   OG1   CG2    CA     gi_2   
[ dihedrals ]
;  ai    aj    ak    al   gromos type
  -CA    -C     N    CA     gd_4   
   -C     N    CA     C     gd_19   
    N    CA     C    +N     gd_20   
    N    CA    CB   OG1     gd_17   
   CA    CB   OG1     P     gd_14   
   CB   OG1     P   O1P     gd_11
  OG1     P   O3P   H3P     gd_11
[ PTRH ]
[ atoms ]
    N     N    -0.28000     0
    H     H     0.28000     0
   CA   CH1     0.00000     1
   CB   CH2     0.00000     1
   CG     C     0.00000     1
  CD1     C    -0.10000     2
  HD1    HC     0.10000     2
  CD2     C    -0.10000     3
  HD2    HC     0.10000     3
  CE1     C    -0.10000     4
  HE1    HC     0.10000     4
  CE2     C    -0.10000     5
  HE2    HC     0.10000     5
   CZ     C     0.00000     6
   OH    OA    -0.36000     6
    P     P     1.23000     6
  O1P    OP    -0.86000     6
  O2P    OP    -0.86000     6
  O3P    OA    -0.54800     6
  H3P     H     0.39800     6
    C     C       0.380     7
    O     O      -0.380     7
[ bonds ]
    N     H    gb_2   
    N    CA    gb_20   
   CA     C    gb_26   
    C     O    gb_4   
    C    +N    gb_9   
   CA    CB    gb_26   
   CB    CG    gb_26   
   CG   CD1    gb_15   
   CG   CD2    gb_15   
  CD1   HD1    gb_3   
  CD1   CE1    gb_15   
  CD2   HD2    gb_3   
  CD2   CE2    gb_15   
  CE1   HE1    gb_3   
  CE1    CZ    gb_15   
  CE2   HE2    gb_3   
  CE2    CZ    gb_15   
   CZ    OH    gb_12   
   OH     P    gb_27   
    P   O1P    gb_23   
    P   O2P    gb_23   
    P   O3P    gb_23   
  O3P   H3P    gb_1
[ exclusions ]
;  ai    aj
   CB   HD1
   CB   HD2
   CB   CE1
   CB   CE2
   CG   HE1
   CG   HE2
   CG    CZ
  CD1   HD2
  CD1   CE2
  CD1    OH
  HD1   CD2
  HD1   HE1
  HD1    CZ
  CD2   CE1
  CD2    OH
  HD2   HE2
  HD2    CZ
  CE1   HE2
  HE1   CE2
  HE1    OH
  HE2    OH
[ angles ]
;  ai    aj    ak   gromos type
   -C     N     H     ga_31   
    H     N    CA     ga_17   
   -C     N    CA     ga_30   
    N    CA     C     ga_12   
   CA     C    +N     ga_18   
   CA     C     O     ga_29   
    O     C    +N     ga_32   
    N    CA    CB     ga_12   
    C    CA    CB     ga_12   
   CA    CB    CG     ga_14   
   CB    CG   CD1     ga_26   
   CB    CG   CD2     ga_26   
  CD1    CG   CD2     ga_26   
   CG   CD1   HD1     ga_24   
  HD1   CD1   CE1     ga_24   
   CG   CD1   CE1     ga_26   
   CG   CD2   HD2     ga_24   
  HD2   CD2   CE2     ga_24   
   CG   CD2   CE2     ga_26   
  CD1   CE1   HE1     ga_24   
  HE1   CE1    CZ     ga_24   
  CD1   CE1    CZ     ga_26   
  CD2   CE2   HE2     ga_24   
  HE2   CE2    CZ     ga_24   
  CD2   CE2    CZ     ga_26   
  CE1    CZ   CE2     ga_26   
  CE1    CZ    OH     ga_26   
  CE2    CZ    OH     ga_26   
   CZ    OH     P     ga_25
   OH     P   O1P     ga_13
   OH     P   O2P     ga_13
   OH     P   O3P     ga_4
  O1P     P   O2P     ga_13
  O1P     P   O3P     ga_13
  O2P     P   O3P     ga_28
    P   O3P   H3P     ga_11
[ impropers ]
;  ai    aj    ak    al   gromos type
    N    -C    CA     H     gi_1   
    C    CA    +N     O     gi_1   
   CA     N     C    CB     gi_2   
   CG   CD1   CD2    CB     gi_1   
  CD2    CG   CD1   CE1     gi_1   
  CD1    CG   CD2   CE2     gi_1   
   CG   CD1   CE1    CZ     gi_1   
   CG   CD2   CE2    CZ     gi_1   
  CD1   CE1    CZ   CE2     gi_1   
  CD2   CE2    CZ   CE1     gi_1   
  CD1    CG   CE1   HD1     gi_1   
  CD2    CG   CE2   HD2     gi_1   
  CE1    CZ   CD1   HE1     gi_1   
  CE2    CZ   CD2   HE2     gi_1   
   CZ   CE1   CE2    OH     gi_1   
[ dihedrals ]
;  ai    aj    ak    al   gromos type
  -CA    -C     N    CA     gd_4   
   -C     N    CA     C     gd_19   
    N    CA     C    +N     gd_20   
    N    CA    CB    CG     gd_17   
   CA    CB    CG   CD1     gd_20   
  CE1    CZ    OH     P     gd_14   
   CZ    OH     P   O1P     gd_11
   OH     P   O3P   H3P     gd_11

; end insert from pamac_hsn.rtp




--------------------------------------------
On Mon, 1/2/16, gromacs.org_gmx-users-request at maillist.sys.kth.se <gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

 Subject: gromacs.org_gmx-users Digest, Vol 142, Issue 1
 To: gromacs.org_gmx-users at maillist.sys.kth.se
 Received: Monday, 1 February, 2016, 9:50 AM
 
 Send gromacs.org_gmx-users mailing
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 than "Re: Contents of gromacs.org_gmx-users digest..."
 
 
 Today's Topics:
 
    1. relative binding free energy
 calculation Gromacs 5.0.5
       (Stefania Evoli)
    2. Re: relative binding free energy
 calculation Gromacs    5.0.5
       (hannes.loeffler at stfc.ac.uk)
    3. gmx sasa (Eric Smoll)
    4. Re: gmx sasa (Justin Lemkul)
    5. g_count (vgsplayer1)
    6. Re: g_count (Mark Abraham)
 
 
 ----------------------------------------------------------------------
 
 Message: 1
 Date: Sun, 31 Jan 2016 12:59:10 +0000
 From: Stefania Evoli <stefania.evoli at kaust.edu.sa>
 To: "gmx-users at gromacs.org"
 <gmx-users at gromacs.org>
 Subject: [gmx-users] relative binding free energy
 calculation Gromacs
     5.0.5
 Message-ID: <D2D3DFC6.41F4%stefania.evoli at kaust.edu.sa>
 Content-Type: text/plain; charset="Windows-1252"
 
 Dear users,
 
 I?m performing relative binding free energy calculation in
 Gromacs 5.0.5. In the mdp files I?m using the following
 section
 
 
 free-energy             
 = yes
 
 init_lambda_state        = LAMBDA
 
 fep_lambdas             
 = 0.0 0.25 0.5 0.75 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0
 1.0  1.0 1.0  1.0 1.0  1.0 1.0  1.0
 
 vdw_lambdas             
 = 0.0 0.00 0.0 0.00 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.65
 0.7 0.75 0.8 0.85 0.9 0.95 1.0
 
 ;couple-moltype       
    = LIG
 
 ;couple-lambda0       
    = vdw-q
 
 ;couple-lambda1       
    = none
 
 ;couple-intramol          = no
 
 sc-alpha             
    = 0.5
 
 sc-sigma             
    = 0.3
 
 sc-power             
    = 1.0
 
 sc-r-power           
    = 6
 
 sc-coul             
     = no
 
 nstdhdl             
     = 100
 
 calc-lambda-neighbors    = -1
 
 
 And I obtained the following values
 
 
  0 -- 1        16.498  +- 
 0.147     16.458  +- 
 0.173     18.142  +- 
 0.465     13.644  +- 
 0.351     16.264  +- 
 0.411     16.264  +-  0.413
 
    1 -- 2     
    7.086  +-  0.143   
   6.982  +-  0.159 
    10.223  +-  0.246   
   4.168  +-  0.299     
 6.971  +-  0.341      6.971 
 +-  0.454
 
    2 -- 3       
 -1.954  +-  0.114 
    -1.685  +-  0.129 
    -1.043  +-  0.574 
    -3.884  +-  0.392 
    -1.883  +-  0.356 
    -1.883  +-  0.356
 
    3 -- 4   
    -13.604  +-  0.139   
 -13.271  +-  0.145    -10.960 
 +-  0.574    -18.048  +- 
 0.234    -14.286  +-  0.601   
 -13.222  +-  0.167
 
    4 -- 5     
    0.089  +-  0.003   
   0.093  +-  0.003     
 0.079  +-  0.005      0.099 
 +-  0.003      0.091  +- 
 0.003      0.085  +-  0.000
 
    5 -- 6     
    0.078  +-  0.004   
   0.079  +-  0.004     
 0.094  +-  0.003      0.062 
 +-  0.008      0.087  +- 
 0.003      0.080  +-  0.000
 
    6 -- 7     
    0.141  +-  0.008   
   0.130  +-  0.011     
 0.110  +-  0.017      0.170 
 +-  0.001      0.170  +- 
 0.001      0.143  +-  0.001
 
    7 -- 8     
    0.123  +-  0.005   
   0.131  +-  0.006     
 0.155  +-  0.001      0.096 
 +-  0.011      0.154  +- 
 0.001      0.121  +-  0.001
 
    8 -- 9     
    0.063  +-  0.005   
   0.063  +-  0.006     
 0.071  +-  0.011      0.056 
 +-  0.001      0.056  +- 
 0.001      0.095  +-  0.001
 
    9 -- 10       
 0.012  +-  0.004      0.002 
 +-  0.005      0.028  +- 
 0.001     -0.004  +- 
 0.008      0.028  +-  0.001 
     0.065  +-  0.001
 
   10 -- 11        0.019 
 +-  0.008      0.030  +- 
 0.011     -0.036  +- 
 0.009      0.084  +-  0.011 
     0.007  +-  0.007     
 0.027  +-  0.001
 
   11 -- 12        0.016 
 +-  0.006      0.013  +- 
 0.007      0.019  +-  0.008 
     0.008  +-  0.009     
 0.018  +-  0.006 
    -0.004  +-  0.000
 
   12 -- 13        0.012 
 +-  0.007      0.015  +- 
 0.008     -0.004  +- 
 0.010      0.028  +-  0.009 
     0.012  +-  0.007 
    -0.018  +-  0.000
 
   13 -- 14       -0.011 
 +-  0.008     -0.010  +- 
 0.009      0.015  +-  0.011 
    -0.034  +-  0.010 
    -0.011  +-  0.008 
    -0.034  +-  0.000
 
   14 -- 15       -0.049 
 +-  0.006     -0.049  +- 
 0.007     -0.055  +- 
 0.014     -0.044  +- 
 0.001     -0.044  +- 
 0.001     -0.054  +-  0.000
 
   15 -- 16       -0.085 
 +-  0.003     -0.086  +- 
 0.004     -0.065  +- 
 0.001     -0.104  +- 
 0.005     -0.066  +- 
 0.001     -0.078  +-  0.001
 
   16 -- 17       -0.116 
 +-  0.009     -0.116  +- 
 0.010     -0.132  +- 
 0.006     -0.100  +- 
 0.016     -0.129  +- 
 0.006     -0.109  +-  0.001
 
   17 -- 18       -0.150 
 +-  0.009     -0.145  +- 
 0.010     -0.129  +- 
 0.018     -0.159  +- 
 0.001     -0.159  +- 
 0.001     -0.151  +-  0.001
 
   18 -- 19       -0.218 
 +-  0.005     -0.220  +- 
 0.005     -0.219  +- 
 0.002     -0.218  +- 
 0.008     -0.219  +- 
 0.002     -0.211  +-  0.001
 
 It is clear the instability of the first four lambda values.
 Can someone suggest me a way to avoid it? I?m trying to use
 different sc-alpha, sc-power and sc-r-power. Any
 suggestion?
 
 Thank you,
 Stefania
 
 ?
 Dr. Stefania Evoli
 Post-Doctoral Fellow
 King Abdullah University of Science and Technology
 Catalysis center - Bldg. 3, 4th floor, 4231?WS18
 Thuwal, Kingdom of Saudi Arabia
 stefania.evoli at kaust.edu.sa
 
 
 
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 ------------------------------
 
 Message: 2
 Date: Sun, 31 Jan 2016 15:13:36 +0000
 From: <hannes.loeffler at stfc.ac.uk>
 To: <gmx-users at gromacs.org>
 Subject: Re: [gmx-users] relative binding free energy
 calculation
     Gromacs    5.0.5
 Message-ID:
     <5FF52965BBB9CB46930C7E5D323EC021E6C99BB1 at EXCHMBX01.fed.cclrc.ac.uk>
 Content-Type: text/plain; charset="Windows-1252"
 
 What do you mean by "instability"?  You also don't
 quite say what these values mean but I guess they are the
 estimates of the free energy per each window as computed by
 different methods(?).  These values come obviously from
 the (linear) electrostatic transformation so playing with
 softcore parameters won't make any difference.
 
 If you are concerned by their magnitudes you can always
 introduce additional lambda points.  BTW, you may want
 to keep the mass-lambdas at their initial values (see
 mailing list archive for details).
 
 ________________________________________
 From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
 [gromacs.org_gmx-users-bounces at maillist.sys.kth.se]
 on behalf of Stefania Evoli [stefania.evoli at kaust.edu.sa]
 Sent: 31 January 2016 12:59
 To: gmx-users at gromacs.org
 Subject: [gmx-users] relative binding free energy
 calculation Gromacs 5.0.5
 
 Dear users,
 
 I?m performing relative binding free energy calculation in
 Gromacs 5.0.5. In the mdp files I?m using the following
 section
 
 
 free-energy             
 = yes
 
 init_lambda_state        = LAMBDA
 
 fep_lambdas             
 = 0.0 0.25 0.5 0.75 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0
 1.0  1.0 1.0  1.0 1.0  1.0 1.0  1.0
 
 vdw_lambdas             
 = 0.0 0.00 0.0 0.00 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.65
 0.7 0.75 0.8 0.85 0.9 0.95 1.0
 
 ;couple-moltype       
    = LIG
 
 ;couple-lambda0       
    = vdw-q
 
 ;couple-lambda1       
    = none
 
 ;couple-intramol          = no
 
 sc-alpha             
    = 0.5
 
 sc-sigma             
    = 0.3
 
 sc-power             
    = 1.0
 
 sc-r-power           
    = 6
 
 sc-coul             
     = no
 
 nstdhdl             
     = 100
 
 calc-lambda-neighbors    = -1
 
 
 And I obtained the following values
 
 
  0 -- 1        16.498  +- 
 0.147     16.458  +- 
 0.173     18.142  +- 
 0.465     13.644  +- 
 0.351     16.264  +- 
 0.411     16.264  +-  0.413
 
    1 -- 2     
    7.086  +-  0.143   
   6.982  +-  0.159 
    10.223  +-  0.246   
   4.168  +-  0.299     
 6.971  +-  0.341      6.971 
 +-  0.454
 
    2 -- 3       
 -1.954  +-  0.114 
    -1.685  +-  0.129 
    -1.043  +-  0.574 
    -3.884  +-  0.392 
    -1.883  +-  0.356 
    -1.883  +-  0.356
 
    3 -- 4   
    -13.604  +-  0.139   
 -13.271  +-  0.145    -10.960 
 +-  0.574    -18.048  +- 
 0.234    -14.286  +-  0.601   
 -13.222  +-  0.167
 
    4 -- 5     
    0.089  +-  0.003   
   0.093  +-  0.003     
 0.079  +-  0.005      0.099 
 +-  0.003      0.091  +- 
 0.003      0.085  +-  0.000
 
    5 -- 6     
    0.078  +-  0.004   
   0.079  +-  0.004     
 0.094  +-  0.003      0.062 
 +-  0.008      0.087  +- 
 0.003      0.080  +-  0.000
 
    6 -- 7     
    0.141  +-  0.008   
   0.130  +-  0.011     
 0.110  +-  0.017      0.170 
 +-  0.001      0.170  +- 
 0.001      0.143  +-  0.001
 
    7 -- 8     
    0.123  +-  0.005   
   0.131  +-  0.006     
 0.155  +-  0.001      0.096 
 +-  0.011      0.154  +- 
 0.001      0.121  +-  0.001
 
    8 -- 9     
    0.063  +-  0.005   
   0.063  +-  0.006     
 0.071  +-  0.011      0.056 
 +-  0.001      0.056  +- 
 0.001      0.095  +-  0.001
 
    9 -- 10       
 0.012  +-  0.004      0.002 
 +-  0.005      0.028  +- 
 0.001     -0.004  +- 
 0.008      0.028  +-  0.001 
     0.065  +-  0.001
 
   10 -- 11        0.019 
 +-  0.008      0.030  +- 
 0.011     -0.036  +- 
 0.009      0.084  +-  0.011 
     0.007  +-  0.007     
 0.027  +-  0.001
 
   11 -- 12        0.016 
 +-  0.006      0.013  +- 
 0.007      0.019  +-  0.008 
     0.008  +-  0.009     
 0.018  +-  0.006 
    -0.004  +-  0.000
 
   12 -- 13        0.012 
 +-  0.007      0.015  +- 
 0.008     -0.004  +- 
 0.010      0.028  +-  0.009 
     0.012  +-  0.007 
    -0.018  +-  0.000
 
   13 -- 14       -0.011 
 +-  0.008     -0.010  +- 
 0.009      0.015  +-  0.011 
    -0.034  +-  0.010 
    -0.011  +-  0.008 
    -0.034  +-  0.000
 
   14 -- 15       -0.049 
 +-  0.006     -0.049  +- 
 0.007     -0.055  +- 
 0.014     -0.044  +- 
 0.001     -0.044  +- 
 0.001     -0.054  +-  0.000
 
   15 -- 16       -0.085 
 +-  0.003     -0.086  +- 
 0.004     -0.065  +- 
 0.001     -0.104  +- 
 0.005     -0.066  +- 
 0.001     -0.078  +-  0.001
 
   16 -- 17       -0.116 
 +-  0.009     -0.116  +- 
 0.010     -0.132  +- 
 0.006     -0.100  +- 
 0.016     -0.129  +- 
 0.006     -0.109  +-  0.001
 
   17 -- 18       -0.150 
 +-  0.009     -0.145  +- 
 0.010     -0.129  +- 
 0.018     -0.159  +- 
 0.001     -0.159  +- 
 0.001     -0.151  +-  0.001
 
   18 -- 19       -0.218 
 +-  0.005     -0.220  +- 
 0.005     -0.219  +- 
 0.002     -0.218  +- 
 0.008     -0.219  +- 
 0.002     -0.211  +-  0.001
 


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