<DIV>Dear Gromacsers,</DIV> <DIV> </DIV> <DIV>I have been doing free energy perturbations Gly->Ala in one strand of collagene.</DIV> <DIV> </DIV> <DIV>Now, the problem is that I have later closely reread the section 5.6.4 ("Free</DIV> <DIV>Energy Calculations") p. 105 in which it says:</DIV> <DIV>"Bonded interactions between atoms that are not perturbed do not need B parameter specifications ..".</DIV> <DIV> </DIV> <DIV>My questions are:</DIV> <DIV>1. Does this mean that bonded interactions between atoms that ARE perturbed DO need B parameter specifications? Even if they are the same in state <BR>A and B?</DIV> <DIV>2. What about the other topology parameters (angles, dihedrals etc), do they need to be specified too?</DIV> <DIV>3. What happens if I have not specified these specifications?</DIV> <DIV> </DIV> <DIV>The relevant parts of the topology file which I use are:</DIV> <DIV> </DIV>
<DIV>[ atoms ]<BR>....</DIV> <DIV> 87 N 13 ALA N 49 -0.28 14.0067 ; qtot 0.72<BR> 88 H 13 ALA H 49 0.28 1.008 ; qtot 1<BR> 89 CH2 13 ALA CA 50 0 14.027 CH1 0.0 3.019 ; qtot 1<BR> 90
DUM 13 ALA CB 50 0 15.035 CH3 0.0 15.035 ; qtot 1<BR> 91 C 13 ALA C 51 0.38 12.011 ; qtot 1.38<BR> 92 O 13 ALA O 51 -0.38 15.9994 ; qtot 1<BR>...</DIV> <DIV> </DIV> <DIV>[ bonds ]<BR>...</DIV> <DIV> 87 89 2 gb_20<BR>
89 90 2 gb_26<BR> 89 91 2 gb_26<BR>...</DIV> <DIV> </DIV> <DIV>[ angles ]</DIV> <DIV>....</DIV> <DIV> 85 87 89 2 ga_30<BR> 88 87 89 2 ga_17<BR> 87 89 90 2 ga_12<BR> 87 89 91 2 ga_12<BR> 90 89 91 2 ga_12<BR> 89 91 92 2 ga_29<BR> 89 91
93 2 ga_18<BR> ....</DIV> <DIV> </DIV> <DIV>And so on, ie, no B specifications have been done except for the atoms!</DIV> <DIV> </DIV> <DIV> </DIV> <DIV>Best regards, and thank you in anticipation,</DIV> <DIV>Soren</DIV> <DIV> </DIV> <DIV> </DIV> <DIV>Ps. One (non-gromacs -sorry) question, given that the above is not wrong:</DIV> <DIV>For the pertubation Gly->Ala I have get a deltaG of 0.8 kcal/mol. Looking through literature, this does not seem all wrong, say if the pertubation took place in an alpha-helix. On the other hand, it is close to the thermal energy (~kT), and a previous article doing the exact same perturbation arrives at a deltaG around 8.6 kcal/mol. Could anyone comment on that?</DIV><p> 
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