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<font style="font-size: 10pt;" face="Verdana" size="2">Hi,</font><font style="font-size: 10pt;" face="Verdana" size="2"><br></font><font style="font-size: 10pt;" face="Verdana" size="2"><br></font><font style="font-size: 10pt;" face="Verdana" size="2">I would also like to be sure that everything works as I have intended it.</font><font style="font-size: 10pt;" face="Verdana" size="2"><br></font><font style="font-size: 10pt;" face="Verdana" size="2">So I guess the following input should work:</font><font style="font-size: 10pt;" face="Verdana" size="2"><br></font><font style="font-size: 10pt;" face="Verdana" size="2">pull = umbrella</font><font style="font-size: 10pt;" face="Verdana" size="2"><br></font><font style="font-size: 10pt;" face="Verdana" size="2">pull_geometry = direction</font><font style="font-size: 10pt;" face="Verdana" size="2"><br></font><font style="font-size: 10pt;" face="Verdana" size="2">pull_dim = N N Y</font><font style="font-size: 10pt;" face="Verdana" size="2"><br></font><font style="font-size: 10pt;" face="Verdana" size="2">pull_start = no</font><font style="font-size: 10pt;" face="Verdana" size="2"><br></font><font style="font-size: 10pt;" face="Verdana" size="2">pull_ngroups = 1</font><font style="font-size: 10pt;" face="Verdana" size="2"><br>pull_group0 = group0</font><font style="font-size: 10pt;" face="Verdana" size="2"><br>pull_group1 = group1</font><font style="font-size: 10pt;" face="Verdana" size="2"><br>pull_init1 = 1.0</font><font style="font-size: 10pt;" face="Verdana" size="2"><br>pull_rate1 = 0</font><font style="font-size: 10pt;" face="Verdana" size="2"><br>pull_k1 = 500.0</font><font style="font-size: 10pt;" face="Verdana" size="2"><br>pull_vec1 = 0 0 1</font><font style="font-size: 10pt;" face="Verdana" size="2"><br>pull_init1 = -1.0</font><font style="font-size: 10pt;" face="Verdana" size="2"><br></font><br>You can also make vec1 -1 and init1 1, but note that also f and dX in the pull output<br>files will then change sign.<br><br>Berk<br><br>> Date: Mon, 16 Nov 2009 01:45:32 -0500<br>> From: chris.neale@utoronto.ca<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] ull code with defined negative relative displacements<br>> <br>> Thank you very much Berk,<br>> <br>> I'm not trying to be argumentative for arguments sake, but I just <br>> can't see how exactly one would make pull_geometry=direction work in <br>> this way. Although I think that I have shown the evidence for this in <br>> my posts, if I am wrong here then clearly I misunderstand something <br>> that is pretty important and, as such, I am keen to stick with this <br>> thread.<br>> <br>> If you have the time to post the entire pull-code portion of the .mdp <br>> options for a pull_geometry=direction run to harmonically restrain <br>> group 1 at a position of 1 nm more negative z in reference to group 0 <br>> then I will do the testing for that setup.<br>> <br>> Nevertheless, I realize that you are very busy and may have more <br>> pressing priorities.<br>> <br>> Thank you for all of your time sticking with this thread for so long,<br>> Chris.<br>> <br>> Hi,<br>> <br>> I would still say pull_geometry=direction would be the easiest <br>> solution for this case,<br>> but pull_geometry=position will probably do the same thing.<br>> <br>> Berk<br>> <br>> [Hide Quoted Text]<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>> 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>> 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>> 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>> 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. 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