[gmx-users] Free Energy of a mutated molecule

[Fabian Casteblanco]

Hello all,

Please if anybody can help.

I'm trying to mutate a -CH3 to an -H (I guess with 3 dummy atoms
attached to it).   Below I sketched the process.   I broke it up into
3 steps  and I wanted to use g_bar for the actual mutation step (step
2).   Does anybody have any experience with something like this?   I
keep getting LINCS errors like this one:

Step 3, time 0.006 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000378, max 0.010709 (between atoms 9 and 68)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
      9     68   57.1    0.1111   0.1099      0.1111
      9     66   90.0    0.1111   0.1122      0.1111

... for some of the Lambdas in the mutation part.  I understand this
is a common error and it means that things are changing so my thinking
is that it is trying to rotate the dummy bonds for some reason I don't
understand.  Are my steps below correct?   Are dummy atoms suppose to
keep their original mass (not zero) ?  Am I suppose to add parameters
for State B for these dummy atom bonds/angles also?

If anybody can help, I would greatly appreciate it.  Thank you.

                                          .--{Atom 68 (H --> Dum)}
                                          |
R - {Atom 8 C} ----- {Atom 9 (C --> H)} ----- {Atom 66 (H --> Dum)}
                                          |
                                          '--{Atom 67 (H --> Dum)}

Essentially.. a R-C-[CH3] --> R-C-[H]

----------------------------------------------------------------------------------------------------------------------------------------------------------

Force Field:  CGenFF

STEP 1:  Decoupling:   -[CH3] (0 Charge, No LJ Interactions)
[ atoms ]
;  nr  type  resnr  resid    atom    cgnr        charge
    mass        typeB  chargeB    massB
....
    8       CG301    1   SIM     C3        8            0.00
    9       CG331    1   SIM     C25      9           -0.27
12.01100      CG331     0.00      12.01100  ;
....
   66      HGA3     1    SIM     H251    66          0.09
1.00800        HGA3      0.00      1.00800    ;
   67      HGA3     1    SIM     H252    67          0.09
1.00800        HGA3      0.00      1.00800    ;
   68      HGA3     1    SIM     H253    68          0.09
1.00800        HGA3      0.00      1.00800    ;

----------------------------------------------------------------------------------------------------------------------------------------------------------

STEP 2:  Mutation:   -[CH3] to -[H]
[ atoms ]
;  nr  type  resnr  resid    atom    cgnr        charge
     mass        typeB  chargeB    massB
    8      CG301    1    SIM      C3        8   	  0.00 		12.01100	
CG311	 0.00	     12.01100      ;
    9      CG331    1    SIM      C25      9	  0.00 	  	12.01100	
HGA1	 0.00	     1.00800	;
....
   66	    HGA3	  1    SIM      H251    66	  0.00   	        1.00800	
DUM	0.00	      0.00	        ;
   67	    HGA3	  1    SIM      H252    67    	  0.00 		1.00800	
DUM	0.00	      0.00	        ;
   68	    HGA3	  1    SIM      H253    68    	  0.00   	
1.00800	   DUM	0.00	      0.00	        ;

----------------------------------------------------------------------------------------------------------------------------------------------------------

STEP 3:  Coupling:   -[H]  (LJ Interactions, Full Charge)
[ atoms ]
;  nr  type  resnr  resid    atom    cgnr        charge
     mass        typeB  chargeB    massB
....
    8     CG311    1    SIM      C3        8   	  0.00 		12.01100	
    CG311	-0.09	   12.01100   ;
    9     HGA1     1    SIM      C25      9	          0.00 	  	
1.00800		 HGA1	 0.09	    1.00800    ;
....
   66	   DUM	 1    SIM     H251    66	  0.00   	         0.00		
 DUM	0.00	     0.00	   ;
   67	   DUM	 1    SIM     H252    67    	  0.00 		 0.00		
DUM	0.00	     0.00	   ;
   68	   DUM	 1    SIM     H253    68    	  0.00   	         0.00		
     DUM	0.00	     0.00	   ;



--
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
E:  fabian.casteblanco at gmail.com