[gmx-users] Re: Free Energy Calculations in Gromacs

[Michael Shirts]

An important final point is that you can always see EXACTLY what
grompp is putting into the B state by running gmxdump on the resulting
tpr.  It's a LOT of information, but all in text all the interactions
are listed explicitly there.

On Mon, Jun 10, 2013 at 6:20 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 6/10/13 2:50 PM, JW Gibbs wrote:
>>
>> Hi,
>>
>> I have been trying to perform the simulations using the amber forcefield,
>> in
>> which the [ pairtypes ] directive is not defined explicitly in the
>> ffnonbonded.itp file, but rather the 1-4 interactions are generated as per
>> the defaults section in the forcefield.itp file. I was wondering what
>> happens to these 1-4 interactions at lambda=1 state?
>>
>> Suppose 1 corresponds to CA and 4 corresponds to NA at state A (lambda =
>> 0)
>> and the CA_per and NA_per are the corresponding atomtypes at state B
>> (lambda
>> = 1).
>>
>> It is defined in the topology file that
>>
>> ...
>> ...
>> [ pairs ]
>>
>> 1      4       1
>> ....
>> ....
>>
>> So does it mean that at state B (lambda = 1), the 1-4 nonbonded
>> interactions
>> will be calculated between CA_per and  NA_per?
>>
>> Although the [ pairs_nb ] section is described in the manual, I would
>> appreciate if someone elaborates a little more.
>>
>
> The actual answer depends on exactly how you're treating the system.  Are
> you using [pairs_nb] in your topology or just [pairs]?  The outcome will be
> different depending on which you're using.  Also note that, as the manual
> says, you don't really need to mess with [pairs_nb] at all; you can achieve
> unscaled internal interactions using "couple-intramol = no" in the .mdp
> file.  Without seeing the .mdp file, it's even more difficult to know what
> you're doing and what you should expect.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
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