On Wed, May 16, 2012 at 4:20 PM, Justin A. Lemkul <[email protected]> wrote:
> > > On 5/16/12 11:16 AM, Steven Neumann wrote: > >> >> >> On Wed, May 16, 2012 at 3:38 PM, Justin A. Lemkul <[email protected] >> <mailto:[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? >> >> > In theory, as long as you've satisfied yourself that this constitutes a > sufficient representation of a non-interacting state, or as close to it as > one can achieve in a system of finite size. I've already said what I think > are reasonable criteria for a preliminary assessment; it's up to you to > convince anyone reading your work that such measurements are sound and > appropriate. > > -Justin Thanks. Well, as my cutoff is 1.4 nm pulling 3.5 nm will suffice - and having the same value in the example makes reasonable argument for pulling e.g. 4nm to be on the safe side. 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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