# Re: detecting vanishing atoms in zero.fep

Date: Wed Oct 31 2018 - 09:06:15 CDT

Please continue all conversations on namd-l. These messages are archived so
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How you assign groups is entirely dependent on: 1) what relative free
energy you wish to compute and 2) how you choose to construct your
topology. There is no single correct answer to this problem.

What specifically do you want to know about this 3-ring structure? I'd
suggest writing out a thermodynamic cycle (or multiple!) and then choosing
endpoints that can be reasonably simulated. You can then assign alchemical
groups to match these endpoints at lambda = 0/1.

BKR

On Tue, Oct 30, 2018 at 6:50 PM soroush ziaei <soroush.ziaei7337_at_gmail.com>
wrote:

> dear brian,
> for a better prespective, we have a structure that contains three aromatic
> ring, so can i divide this three groups into -1,1,0 ?
> or in another words we have a lot of structures that has a symmetry. for
> this item can i choose number <1> for one side?
>
> On Mon, Oct 29, 2018 at 11:51 AM soroush ziaei <
> soroush.ziaei7337_at_gmail.com> wrote:
>
>> this problem under consideration! what do you mean brian?
>> meanwhile in this .rtf file (topology), can i put -1 & 1 for CG2R61
>> (C2-C14) and HGR61 respectively?
>>
>> # CGENFF.rtf
>>
>> RESI ***** 0.000 ! param penalty= 78.400 ; charge penalty= 25.148
>> GROUP ! CHARGE CH_PENALTY
>> ATOM N1 NG2R51 -0.169 ! 25.148
>> ATOM N2 NG2R50 -0.559 ! 5.159
>> ATOM N3 NG2R50 -0.662 ! 0.474
>> ATOM N4 NG1T1 -0.463 ! 0.000
>> ATOM N5 NG1T1 -0.463 ! 0.000
>> ATOM C1 CG311 0.289 ! 24.191
>> ATOM C2 CG2R61 -0.005 ! 14.165
>> ATOM C3 CG2R61 -0.005 ! 14.165
>> ATOM C4 CG2R61 -0.115 ! 6.325
>> ATOM C5 CG2R61 -0.115 ! 6.325
>> ATOM C6 CG2R61 -0.115 ! 6.325
>> ATOM C7 CG2R61 -0.115 ! 6.325
>> ATOM C8 CG2R53 0.266 ! 5.687
>> ATOM C9 CG2R61 -0.104 ! 0.000
>> ATOM C10 CG2R61 -0.104 ! 0.000
>> ATOM C11 CG2R61 -0.104 ! 0.000
>> ATOM C12 CG2R61 -0.104 ! 0.000
>> ATOM C13 CG2R61 0.095 ! 0.000
>> ATOM C14 CG2R61 0.095 ! 0.000
>> ATOM C15 CG2R53 0.468 ! 2.500
>> ATOM C16 CG1N1 0.356 ! 0.000
>> ATOM C17 CG1N1 0.356 ! 0.000
>> ATOM H1 HGA1 0.090 ! 0.601
>> ATOM H2 HGR61 0.115 ! 0.000
>> ATOM H3 HGR61 0.115 ! 0.000
>> ATOM H4 HGR61 0.115 ! 0.000
>> ATOM H5 HGR61 0.115 ! 0.000
>> ATOM H6 HGR52 0.157 ! 0.684
>> ATOM H7 HGR61 0.115 ! 0.000
>> ATOM H8 HGR61 0.115 ! 0.000
>> ATOM H9 HGR61 0.115 ! 0.000
>> ATOM H10 HGR61 0.115 ! 0.000
>> ATOM H11 HGR52 0.110 ! 0.000
>>
>> On Sun, Oct 28, 2018 at 7:09 PM Brian Radak <brian.radak_at_gmail.com>
>> wrote:
>>
>>> Your question seems entirely dependent on the problem under
>>> consideration.
>>>
>>> Atoms with a flag of 1 get scaled as a function of alchLambda while
>>> those with a flag of -1 get scaled as a function of 1-alchLambda. If you
>>> swap the groups you just change the sign of the free energy that is
>>> computed, so this is somewhat arbitrary and/or a matter of bookkeeping.
>>>
>>> HTH,
>>> BKR
>>>
>>> On Sat, Oct 27, 2018, 4:39 PM soroush ziaei <soroush.ziaei7337_at_gmail.com>
>>> wrote:
>>>
>>>> hi all,
>>>> i want to know how can i detect which atom should be -1 in fep file in
>>>> order to obtain correct value for delta<g>?
>>>> or please describe some method to generate topology file for a unique
>>>> structure, such as topology file that exist in tutorial (zero.top).
>>>>
>>>> best regards,
>>>> soroush
>>>>
>>>

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