On Wed, May 16, 2012 at 3:38 PM, Justin A. Lemkul <[email protected]> wrote:
> > > On 5/16/12 10:25 AM, Steven Neumann wrote: > >> Dear Justin, >> >> I pulled my ligad away of 6nm from the protein and obtained beautiful and >> smooth >> curve of PMF using 28 windows. Starting from zero kcal/mol corresponding >> to app >> 0.3 nm then minima and curve increase till my plateau which starts from >> app 1 nm >> - then I have nearly straight line till 6.3 nm. >> My question: Can I decrease pulling distance to save time for the future >> simualtions with this system in terms of number of water molecules? Shall >> I just >> pull it away of 2-3 nm and I will obtain the same deltaG? >> >> > Ideally, one would separate the molecules such that they are no longer > interacting. Obviously with methods like PME this is impossible, so what > you're after is sufficient separation such that there is negligible > interaction between the protein and ligand. The required distance depends > on the nature and size of the ligand, the types of interactions it > experiences, and the cutoffs used. Keep in mind that even if a molecule is > beyond the longest nonbonded cutoff, there are still effects like water > ordering that can persist up to about 1.0 nm, so I would certainly make > sure that all the atoms of the ligand and protein are separated by a > minimum of twice the longest cutoff or so to account for this effect. Note > that this would imply the use of g_mindist, not g_dist, as the distance I'm > talking about is not the same as the COM distance. > > That's just my own rule of thumb for an initial check; you'll have to > analyze your own system to decide what's happening and what you should do. > > -Justin > Thanks Justin! I totally agree. But now having my ligand pulled 6 nm away and obtained deltaG= -4.5 kcal/mol. In theory when I use all windows till 3.5 nm (not till 6.3 nm) and I will obtain the same value it means that I can decrease the pulling distance in future simulations. Am I right? Steven > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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