Hi,
I use thermodynamics integration.
The protocol is 1000step energy minimization, 20 ps bond-constraint MD,
and then 200ps MD for collecting dgdl.
thanks
Qiang
Gerrit Groenhof wrote:
Looks like hysteresis. Do you do slow growth, or discrete FEP?
Gerrit
Dear all Gmxers,
I am calculating a mutation free energy from L<->A for a five AA
peptides using G96 53a6 force field.
however, my dG_for and dG_rev is quite different.
dG_for(lambda=0.00) = - 9.9 kJ/mol
dG_rev(lambda=1.00) = 1.33 kJ/mol
Is there anything wrong with setting up topologies?
Here is the [atoms] part for morphed atoms. and I attached the full
.top in the attachment.
For L->A:
[ atoms ]
17 CH2 2 LEU CB 6 0
14.027 CH3 0 15.035; qtot 1
18 CH1 2 LEU CG 7 0
13.019 DUM 0 13.019; qtot 1
19 CH3 2 LEU CD1 7 0
15.035 DUM 0 15.035; qtot 1
20 CH3 2 LEU CD2 7 0
15.035 DUM 0 15.035; qtot 1
For A->L :
[ atoms ]
17 CH3 2 ALA CB 6 0
15.035 CH2 0 14.027; qtot 1
60 DUM 6 DUM DUM 24 0
13.019 CH1 0 13.019
61 DUM 6 DUM DUM 24 0
15.035 CH3 0 15.035
62 DUM 6 DUM DUM 24 0
15.035 CH3 0 15.035
thanks for help
LQ
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