[gmx-users] mass changes in free energy calculations

friendli friendli2000 at gmail.com
Fri Jun 13 09:04:31 CEST 2008

Dear all,

I am calculating FE using TI. I have a question about mutating existing 
atoms with different mass.
for example, using ffG53a6 force field, in one case i need to mutate CH2 
to CH3,
should I use
[ atoms ]
 17        CH3      2    ALA     CB      6          0     15.035     
CH2    0    14.027; qtot 1


 17        CH3      2    ALA     CB      6          0     15.035     
CH2    0    15.035; qtot 1

I notice from Prof. Alan Mark's online FE course, he mutates a H atom to 
a O atom, but does not change its mass.
The line is :
12    HC        1     PHE       HZ          6           0.1        
1.008       OA         -0.548        1        1.008

Can somebody explain a bit why we should not change the mass accordingly?

thank you


I though I sent this email but why I can not see it. There may be 
something wrong with my email software. so I send here again. sorry

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