Are you sure you need TI for this? Looks to me that what you need to
do is "rerun" this with imin=5 with sander with exactly the same
protocol you have used in the original perturbations but without
invoking TI. Both end states are the unperturbed states so I don't see
the need for TI. Then grep the energies and plug them into the
exponential formula accordingly.
On Thu, 2 Apr 2015 12:57:35 +0200
<vladimir.palivec.marge.uochb.cas.cz> wrote:
> Hello again,
>
> I am wondering if anyone has encountered this before. Basically what
> I am trying to do is this :
>
> http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme
>
> to calculate binding energy of a ligand to protein. I have done
> almost all the steps, however, i would like also to do long range
> dispersion correction. In order to do this, you have to rerun your
> simulation at lambda = 1 and lambda = 0 with different cut-offs (eg.
> 9A and 30A). In other words, I want to calculate energy of a system
> at each step within certain trajectory using cutoff1 = 9A and cutoff2
> = 10A and compare the results. However, I have not found any way to
> do this. I assume to somehow utilize imin=5 with thermodynamic
> integration (I have done calculations using pmemd, but pmemd does no
> support imin=5), and sander.
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Received on Thu Apr 02 2015 - 05:00:02 PDT
