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.castebla...@gmail.com
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