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Hi,<br><br>pull_init should be 1, not 4.75, if you want group1 to be 1 nm below group0.<br>Alternatively you can have vec = 0 0 1 and pull_init = -1.<br><br>Berk<br><br>> Date: Sat, 14 Nov 2009 14:54:54 -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 Justin, (comment to Berk below)<br>> <br>> thanks for pointing out the g_wham problem. I am personally ok here as <br>> I use a non-gromacs wham program.<br>> <br>> Hi Berk,<br>> <br>> unless I misunderstood, your suggestion does not yield the gromacs 3 <br>> behaviour that I am trying to reproduce with gromacs 4.<br>> <br>> If I simply misunderstood your suggestion, can you please be a little <br>> more explicit? What I want to do is to harmonically restrain the COM <br>> of group 1 to be X nm more negative along Z than the COM of group 0. <br>> It is important that this still works when the value for X is smaller <br>> than the standard deviation of the sampled values such that the <br>> distribution does not become bimodal.<br>> <br>> Here is the test using pull_geometry=direction, and I note that this <br>> is exactly the same behaviour that I observed and posted in my last <br>> email while using pull_geometry=distance in combination with pull_vec.<br>> <br>> pull = umbrella<br>> pull_geometry = direction<br>> pull_dim = N N Y<br>> pull_start = no<br>> pull_nstxout = 10<br>> pull_nstfout = 10<br>> pull_ngroups = 1<br>> pull_group0 = POPC<br>> pull_pbcatom0 = 0<br>> pull_group1 = Protein<br>> pull_pbcatom1 = 0<br>> pull_init1 = 4.75<br>> pull_rate1 = 0<br>> pull_k1 = 500.0<br>> pull_vec1 = 0 0 -1<br>> <br>> <br>> coord.xvg:<br>> 1669.4000 4.97979 -4.68988<br>> force.xvg:<br>> 1669.4000 30.0622<br>> Where the force should be -30.062 (assuming that I understand <br>> everything correctly).<br>> <br>> coord.xvg:<br>> 2.9600 5.16151 -5.14321<br>> force.xvg<br>> 2.9600 -196.603<br>> Where the force should be +196.603 (assuming that I understand <br>> everything correctly).<br>> <br>> pull = umbrella<br>> pull_geometry = direction<br>> pull_dim = N N Y<br>> pull_start = no<br>> pull_nstxout = 10<br>> pull_nstfout = 10<br>> pull_ngroups = 1<br>> pull_group0 = POPC<br>> pull_pbcatom0 = 0<br>> pull_group1 = Protein<br>> pull_pbcatom1 = 0<br>> pull_init1 = 4.75<br>> pull_rate1 = 0<br>> pull_k1 = 500.0<br>> pull_vec1 = 0 0 1<br>> <br>> coord.xvg:<br>> 0.5200 5.17421 5.00621<br>> force.xvg:<br>> 0.5200 -128.107<br>> Where this is what I intend to occur (i.e. working as I desire it to).<br>> <br>> coord.xvg:<br>> 1649.4000 4.99895 4.69239<br>> force.xvg:<br>> 1649.4000 28.807<br>> Where this is what I intend to occur (i.e. working as I desire it to).<br>> <br>> <br>> <br>> <br>> Thank you,<br>> Chris.<br>> <br>> --- original message --<br>> <br>> Hi,<br>> <br>> You should use pull_geometry=direction.<br>> distances don't get negative.<br>> <br>> Berk<br>> <br>> > Date: Sat, 14 Nov 2009 09:21:39 -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>> > Hello, I am re-running some of our gromacs 3 simulations using gromacs<br>> > 4, and as far as I can tell the gromacs 4 pull code, while very nicely<br>> > enhanced from gromacs 3, has also lost some functionality.<br>> ><br>> > I am calculating the PMF of a peptide across a bilayer and, to <br>> > simplify the issue, what I can't figure out how to do with gromacs 4 <br>> > is to pull group1 to a position 1 nm more negative along the z-axis <br>> > than group 0 (the bilayer in this case) for some replicas and to 1 <br>> > nm more positive along the z-axis than group 0 in others. I'll <br>> > focus on the negative displacement here as it is the one that is <br>> > giving me problems.<br>> ><br>> > This used to be possible with the following gromacs 3 pull.ppa options:<br>> ><br>> > runtype = umbrella<br>> > reftype = com<br>> > pulldim = N N Y<br>> > reference_group = group0<br>> > group_1 = group1<br>> > K1 = 500<br>> > Pos1 = 0 0 -1.0<br>> ><br>> > Sure, I could start group1 in the correct negative-z displacement from<br>> > group0 and use pull_init1=+1.0, but this will not work when, for<br>> > instance, I want to restrain it to -0.1 nm (using pull_init1=+0.1),<br>> > where the sampling will infrequently jump back and forth about z=0.<br>> ><br>> > Just to be sure, I tried for gromacs 4 are the following pull code <br>> > .mdp options:<br>> ><br>> > pull = umbrella<br>> > pull_geometry = distance<br>> > pull_dim = N N Y<br>> > pull_start = no<br>> > pull_ngroups = 1<br>> > pull_group0 = group0<br>> > pull_group1 = group1<br>> > pull_init1 = -1.0<br>> > pull_rate1 = 0<br>> > pull_k1 = 500.0<br>> ><br>> > where mdrun complains:<br>> > "Pull reference distance for group 1 is negative (-1.000000)"<br>> ><br>> > and it is pretty obvious why this doesn't work since it is asking for<br>> > a negative displacement. Nevertheless, I tried it and pull_init1<br>> > appears to get set to zero.<br>> ><br>> > I also attempted the following.<br>> ><br>> > pull = umbrella<br>> > pull_geometry = distance<br>> > pull_dim = N N Y<br>> > pull_start = no<br>> > pull_ngroups = 1<br>> > pull_group0 = group0<br>> > pull_group1 = group1<br>> > pull_init1 = 1.0<br>> > pull_rate1 = 0<br>> > pull_k1 = 500.0<br>> > pull_vec1 = 0 0 -1<br>> ><br>> > where I would then use<br>> > pull_init1 = 1.0<br>> > pull_vec1 = 0 0 1<br>> > for the positive side of the bilayer.<br>> ><br>> > However, when I look at the forces, I am getting the negative of <br>> > what I should get when pull_vec1 = 0 0 -1.<br>> ><br>> > coord.xvg:<br>> > 610.0000 4.9343 -1.02019<br>> > 660.0001 4.91454 -0.949747<br>> ><br>> > force.xvg:<br>> > 610.0000 -10.0932<br>> > 660.0001 25.1265<br>> ><br>> > Although I am getting exactly what I should get when pull_vec1 = 0 0 <br>> > 1 (for intended positive displacements).<br>> ><br>> > coord.xvg:<br>> > 660.0001 4.9014 1.16304<br>> ><br>> > force.xvg:<br>> > 660.0001 -81.5201<br>> ><br>> > Any ideas are greatly appreciated. I can probably mod the code for my<br>> > needs, but a standard gromacs binary is always preferable.<br>> ><br>> > Thank you,<br>> > Chris.<br>> ><br>> ><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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