[gmx-users] soft-core and coulomb transformation

[bharat v. adkar]

On Mon, 5 Nov 2007, David Mobley wrote:

> Hi,
>
>> Everything goes fine till this point. Now, i do reverse transformations to
>> check for hysteresis. For vdw transformations, i get almost perfect
>> overlap of dG/dlambda vs lambda for forward and reverse transformations,
>> but for coloumb transformations, if i don't use soft-core potentials, i
>> don't get any overlap (i understand that getting overlap in forward and
>> reverse transformations is not the accurate-enough measure of absence of
>> hysteresis, but for smaller systems 5 ns at each lambda value should be
>> sufficiently enough sampling).
>
> I am not sure what you mean by "directions". Can you clarify your
> protocol? For example, the protocol used in my tutorial has no
> directionality. The only way I can think of you having directionality
> is if you are either:
> (a) Using "slow growth" where lambda is a function of time
> (b) Running your simulations consecutively, where the simulation at
> each lambda value begins from the endpoint of the simulation at the
> previous lambda value.
>
> Neither of those is what I would particularly recommend, since both
> introduce additional hysteresis. I'd instead recommend running
> independent equilibrium simulations at different lambda values, making
> sure you equilibrate long enough at each.

it is fairly straight FORWARD.. forward is from state A to state B, and 
reverse is from state B to state A. Say for example, forward 
transformation is going from ethane to methane. in this step, i define 
three of the terminal hydrogen on say C2, with zero charges and C2 with 
charge of hydrogen in B state having their vdw terms unchanged. During 
forward transformation of coulombs, i modify these charges with 15 lambda 
values inclusive of 0 and 1. simulations at each lambda value are 
independent of each other, i.e., starts with the same starting structure. 
simulation protocol at each lambda value has energy minimization, 20 ps 
equilibration, and 5 ns production steps.

similarly, reverse transformation means going from methane to ethane.

i am pasting the part of topology used for charge transformation:

#ifdef coul_fwd
1 opls_135 1 ETH   CA1  1 -0.18  12.011 opls_138 -0.24  12.011 
2 opls_140 1 ETH  HA11  1  0.06   1.008
3 opls_140 1 ETH  HA12  1  0.06   1.008
4 opls_140 1 ETH  HA13  1  0.06   1.008
5 opls_135 1 ETH   CA2  1 -0.18  12.011 opls_135  0.06  12.011
6 opls_140 1 ETH  HA21  1  0.06   1.008 opls_140  0      1.008
7 opls_140 1 ETH  HA22  1  0.06   1.008 opls_140  0      1.008
8 opls_140 1 ETH  HA23  1  0.06   1.008 opls_140  0      1.008
#endif
#ifdef coul_rev
1 opls_138 1 ETH   CA1  1 -0.24  12.011 opls_135 -0.18  12.011
2 opls_140 1 ETH  HA11  1  0.06   1.008
3 opls_140 1 ETH  HA12  1  0.06   1.008
4 opls_140 1 ETH  HA13  1  0.06   1.008
5 opls_135 1 ETH   CA2  1  0.06  12.011 opls_135 -0.18  12.011
6 opls_140 1 ETH  HA21  1  0      1.008 opls_140  0.06   1.008
7 opls_140 1 ETH  HA22  1  0      1.008 opls_140  0.06   1.008
8 opls_140 1 ETH  HA23  1  0      1.008 opls_140  0.06   1.008
#endif

the change from opls_135 to opls_138 is silent, i.e., both have same 
atomtype and same nonbonded parameters.

I hope i have explained the protocol in detail.


>
>> My doubt is why should this happen? if there is no problem like
>> singularities in potentials, why should not using sc-potentials make
>> such a difference?
>
> To clarify, you want to NOT use soft core potentials for
> electrostatics, and use SC for the LJ transformation.

that is what i am doing. i am using SC for vdw (LJ) transformation and no 
SC for charge transformation. My observation is i do not get overlap of 
dG/dl vs lambda curves when i do "forward" and "reverse" transformation 
(i hope, my definitions of forward and reverse are clear by now) of 
charges. but when i use SC while coulomb transforamtion also, as in LJ 
transformation, the curves overlap. Now the question is why is it 
necessary to use SC during charge transformation to get overlap of the 
curves. It makes no sense at least to me.

please help.

bharat


>
> You need to provide more detail on your protocol.
>
> David
>
>> i tried this for simple ala->gly and ethane->methane transformations.
>>
>> please give me some insight into the problem...
>>
>> bharat
>>
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