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Hi,<br><br>I would still say pull_geometry=direction would be the easiest solution for this case,<br>but pull_geometry=position will probably do the same thing.<br><br>Berk<br><br>> Date: Sun, 15 Nov 2009 17:11:43 -0500<br>> From: chris.neale@utoronto.ca<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] pull code with defined negative relative displacements<br>> <br>> Hi Berk,<br>> <br>> I do not mean the box 0, and I am aware about the pull distance <br>> needing to be less than half of the smallest box length. Please allow <br>> me describe a bit more rigorously what I need to avoid. I will use an <br>> example that is totally fictitious, but is designed to emphasize the <br>> bimodal sampling issue that is relevant to my actual study.<br>> <br>> 1. Imagine that one wants to calculate the PMF for a water molecule <br>> along the normal to an asymmetric bilayer in which one leaflet is POPC <br>> and the other is lipidA.<br>> <br>> 2. The free energy for that water residing 0.1 nm away from the <br>> bilayer center in the POPC leaflet (call it -0.1 nm from the bilayer <br>> center) needs to be calculated separately from the free energy for <br>> that water residing 0.1 nm away from the bilayer center in the lipidA <br>> leaflet (call it +0.1 nm from the bilayer center).<br>> <br>> 3. Let the force constant be 500 kJ/mol/nm^2 and let the user apply <br>> pull_geometry=distance and pull_init1=0.1 while starting the replica <br>> at 0.1 nm from the bilayer center in two simulations where one takes <br>> (a) a starting water position that is 0.1 nm toward the POPC <br>> headgroups and the other takes (b) a starting position of the water to <br>> be 0.1 nm toward the lipidA headgroups.<br>> <br>> 4. I posit that the probability distributions of the water about the <br>> bilayer normal from simulations (a) and (b) in part 3 above will <br>> converge to the same distribution and that this distribution will be <br>> bimodal with one peak at -0.1 nm and one peak at +0.1 nm. This is <br>> because the simulation that started at -0.1 (0.1 nm closer to the POPC <br>> headgroups) will, even under the biasing force, infrequently cross the <br>> bilayer center of mass and then be closer to the lipidA heagroups. At <br>> this point. the direction of the applied force will the change to draw <br>> the water toward the other possible location at +0.1 nm.<br>> <br>> 5a. For displacements >> 0.1 nm, this will not be a problem.<br>> 5b. For larger force constants, this will not be a problem at 0.1 nm, <br>> but will still be a problem for some closer centers of restraint.<br>> <br>> 6. pull_geometry=distance is entirely incompatible with this approach.<br>> <br>> 7. pull_geometry=position does appear to work.<br>> <br>> <br>> Thanks for your patience,<br>> Chris.<br>> <br>> -- original message --<br>> <br>> Hi,<br>> <br>> Sorry, but I have no clue what you mean with sampling >0<br>> and how you would end up with a bimodal distribution.<br>> <br>> You don't mean the box 0, do you?<br>> That is irrelevant.<br>> What can be a problem is that you pull distance should not be more <br>> than half the box length.<br>> <br>> Berk<br>> <br>> > Date: Sun, 15 Nov 2009 12:33:30 -0500<br>> > From: chris.neale at utoronto.ca<br>> > To: gmx-users at gromacs.org<br>> > Subject: [gmx-users] pull code with defined negative relative displacements<br>> ><br>> > > I only now noticed Justin mail on g_wham.<br>> > > You can probably also use pull_geometry=distance and pull_init=1,<br>> > > if you starting structure has group1 close to 1 nm below group 0.<br>> ><br>> > Agreed, although this will not work when the force constant is not <br>> > strong enough to inhibit any sampling >0 -- wherein the distribution <br>> > about 0 would become bimodal and this is something that I can not <br>> > allow.<br>> ><br>> > As far as I can tell, pull_geometry=position, pull_init1<0, and <br>> > pull_vec1=0 0 0 is the solution, as per my previous message.<br>> ><br>> > Thank you,<br>> > Chris.<br>> <br>> <br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>                                            <br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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