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Hi,<br><br>With only 1 pull dimension active (through pull_dims) all three geometries are equivalent.<br>In 2 or 3D there are all different.<br><br>With pull_geometry=direction the pull force is the force working along the direction vector.<br>So in general you can't incorporate the direction (only sign in your case) into the force,<br>unless you would print the whole vector.<br><br>Berk<br><br>> Date: Wed, 18 Nov 2009 12:12:49 -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 have done the tests and you are entirely correct. I have one further <br>> question: If I simply want to pull to a relative displacement of -1.0 <br>> nm, is there any reason to prefer one of these methods, or are they <br>> just overlapping implementations of different methods that also have <br>> unique abilities given other settings?<br>> <br>> To summarize my tests, pull_geometry=direction can indeed pull to negative <br>> displacements and there is no bimodal behaviour. My misunderstanding <br>> derived from the fact that<br>> <br>> pull_geometry = direction<br>> pull_init1 = 1.0<br>> pull_vec1 = 0 0 1<br>> <br>> gave the forces as I expected them, while<br>> <br>> pull_vec1 = 0 0 -1<br>> <br>> reports the negative of the force that I expected. Since the force as <br>> output is probably applied after multiplication by pull_vec1, it might <br>> be more intuitive to simply output the force after it is multiplied by <br>> pull_vec1 such that what is output is the actual applied force. But <br>> then again there are probably some good reasons why it is output the <br>> way that it is.<br>> <br>> I have included probability distribution plots for the sampling along z for the tests below at:<br>> http://i205.photobucket.com/albums/bb192/chrisneale_2007/X10.png (1.0 nm displacement test)<br>> http://i205.photobucket.com/albums/bb192/chrisneale_2007/X005.png (0.05 nm displacement test)<br>> http://i205.photobucket.com/albums/bb192/chrisneale_2007/X35.png (3.5 nm displacement test)<br>> <br>> Thank you for all of your assistance,<br>> Chris.<br>> <br>> #####################<br>> Summary for attempts to pull to -1.0:<br>> <br>> ### Pulls to -1<br>> <br>> pull_geometry = position<br>> pull_init1 = 0 0 -1<br>> pull_vec1 = 0 0 0<br>> <br>> pull_geometry = direction<br>> pull_init1 = -1.0<br>> pull_vec1 = 0 0 1<br>> <br>> pull_geometry = direction<br>> pull_init1 = 1.0<br>> pull_vec1 = 0 0 -1<br>> <br>> ### Pulls to +1<br>> <br>> pull_geometry = direction<br>> pull_init1 = 1.0<br>> pull_vec1 = 0 0 1<br>> <br>> #####################<br>> Detailed results:<br>> <br>> pull_geometry = position<br>> pull_init1 = 0 0 -1<br>> pull_vec1 = 0 0 0<br>> <br>> $ tail coord.xvg<br>> 98.2000        5.03064        -0.96114<br>> 98.4000        5.02906        -0.968864<br>> 98.6000        5.02755        -1.0196<br>> 98.8000        5.02577        -0.971355<br>> 99.0000        5.02408        -0.948518<br>> 99.2000        5.02289        -0.973627<br>> 99.4000        5.0227        -0.977471<br>> 99.6000        5.02293        -0.965711<br>> 99.8000        5.0242        -1.01475<br>> 100.0000        5.0251        -1.03216<br>> <br>> $ tail force.xvg<br>> 98.2000        -19.4299<br>> 98.4000        -15.568<br>> 98.6000        9.8014<br>> 98.8000        -14.3227<br>> 99.0000        -25.741<br>> 99.2000        -13.1865<br>> 99.4000        -11.2644<br>> 99.6000        -17.1443<br>> 99.8000        7.37747<br>> 100.0000        16.0813<br>> <br>> ########################################<br>> <br>> pull_geometry = direction<br>> pull_init1 = 1.0<br>> pull_vec1 = 0 0 1<br>> <br>> $ tail coord.xvg<br>> 98.2000        5.06691        1.09005<br>> 98.4000        5.06773        1.04829<br>> 98.6000        5.06842        1.02481<br>> 98.8000        5.06934        1.02874<br>> 99.0000        5.07061        0.995157<br>> 99.2000        5.07164        0.990872<br>> 99.4000        5.07205        1.00651<br>> 99.6000        5.07256        1.02346<br>> 99.8000        5.07107        0.986439<br>> 100.0000        5.06931        1.03009<br>> <br>> $ tail force.xvg<br>> 98.2000        -45.0273<br>> 98.4000        -24.1432<br>> 98.6000        -12.4043<br>> 98.8000        -14.3716<br>> 99.0000        2.42147<br>> 99.2000        4.56404<br>> 99.4000        -3.25742<br>> 99.6000        -11.7324<br>> 99.8000        6.78027<br>> 100.0000        -15.0443<br>> <br>> ### where it does start at -1.0<br>> <br>> $ grep -v '[#|@]' coord.xvg |head<br>> 0.0000        5.05992        -1.09968<br>> 0.2000        5.05948        -0.473992<br>> 0.4000        5.05982        0.43101<br>> 0.6000        5.06017        0.77986<br>> 0.8000        5.0609        0.78875<br>> 1.0000        5.06113        0.75552<br>> 1.2000        5.06151        0.750633<br>> 1.4000        5.06086        0.79958<br>> 1.6000        5.05976        0.821069<br>> 1.8000        5.05811        0.950296<br>> <br>> ###############################<br>> <br>> pull_geometry = direction<br>> pull_init1 = -1.0<br>> pull_vec1 = 0 0 1<br>> <br>> $ tail -n 30 coord.xvg|head -n 10<br>> 94.2000        5.04636        -1.00959<br>> 94.4000        5.04605        -1.09414<br>> 94.6000        5.04503        -1.09134<br>> 94.8000        5.0431        -1.10409<br>> 95.0000        5.04174        -1.05292<br>> 95.2000        5.04012        -1.03421<br>> 95.4000        5.03944        -1.05723<br>> 95.6000        5.03981        -1.00803<br>> 95.8000        5.04072        -1.01506<br>> 96.0000        5.04055        -0.980655<br>> <br>> $ tail -n 30 force.xvg|head -n 10<br>> 94.2000        4.79288<br>> 94.4000        47.0722<br>> 94.6000        45.6695<br>> 94.8000        52.0426<br>> 95.0000        26.4623<br>> 95.2000        17.107<br>> 95.4000        28.6127<br>> 95.6000        4.0165<br>> 95.8000        7.52866<br>> 96.0000        -9.67265<br>> <br>> ###############################<br>> <br>> pull_geometry = direction<br>> pull_init1 = 1.0<br>> pull_vec1 = 0 0 -1<br>> <br>> $ tail coord.xvg<br>> 98.2000        5.01781        -1.04195<br>> 98.4000        5.01766        -0.988034<br>> 98.6000        5.01789        -0.963644<br>> 98.8000        5.0185        -0.980899<br>> 99.0000        5.01958        -0.917222<br>> 99.2000        5.021        -1.00548<br>> 99.4000        5.02016        -0.970434<br>> 99.6000        5.01848        -1.01137<br>> 99.8000        5.01723        -0.950541<br>> 100.0000        5.01743        -1.01916<br>> <br>> $ tail force.xvg<br>> 98.2000        -20.9744<br>> 98.4000        5.98316<br>> 98.6000        18.1779<br>> 98.8000        9.55039<br>> 99.0000        41.3892<br>> 99.2000        -2.73847<br>> 99.4000        14.7832<br>> 99.6000        -5.68352<br>> 99.8000        24.7297<br>> 100.0000        -9.58189<br>> <br>> #####################<br>> #####################<br>> #####################<br>> #####################<br>> <br>> Summary for attempts to pull to -0.1:<br>> <br>> ### Pulls to -0.1<br>> <br>> pull_geometry = position<br>> pull_init1 = 0 0 -0.1<br>> pull_vec1 = 0 0 0<br>> <br>> pull_geometry = direction<br>> pull_init1 = -0.1<br>> pull_vec1 = 0 0 1<br>> <br>> <br>> pull_geometry = direction<br>> pull_init1 = 0.1<br>> pull_vec1 = 0 0 -1<br>> <br>> ### Pulls to +0.1<br>> <br>> pull_geometry = direction<br>> pull_init1 = 0.1<br>> pull_vec1 = 0 0 1<br>> <br>> #####################<br>> Detailed results:<br>> <br>> pull_geometry = position<br>> pull_init1 = 0 0 -0.1<br>> pull_vec1 = 0 0 0<br>> <br>> $ tail coord.xvg<br>> 98.2000        5.05551        -0.0467954<br>> 98.4000        5.05655        -0.0756043<br>> 98.6000        5.05742        -0.132113<br>> 98.8000        5.05886        -0.182411<br>> 99.0000        5.05929        -0.148237<br>> 99.2000        5.05957        -0.0355667<br>> 99.4000        5.06157        0.00486353<br>> 99.6000        5.06353        0.0215776<br>> 99.8000        5.06373        -0.0272107<br>> 100.0000        5.06301        -0.157927<br>> <br>> $ tail force.xvg<br>> 98.2000        -26.6023<br>> 98.4000        -12.1979<br>> 98.6000        16.0563<br>> 98.8000        41.2056<br>> 99.0000        24.1184<br>> 99.2000        -32.2166<br>> 99.4000        -52.4318<br>> 99.6000        -60.7888<br>> 99.8000        -36.3946<br>> 100.0000        28.9634<br>> <br>> ########################################<br>> <br>> pull_geometry = direction<br>> pull_init1 = 0.1<br>> pull_vec1 = 0 0 1<br>> <br>> $ tail coord.xvg<br>> 98.2000        5.03896        -0.0415608<br>> 98.4000        5.03914        -0.0285805<br>> 98.6000        5.03966        0.0746529<br>> 98.8000        5.03966        0.22066<br>> 99.0000        5.04063        0.254914<br>> 99.2000        5.04097        0.0771699<br>> 99.4000        5.03999        -0.0702654<br>> 99.6000        5.04055        -0.0993152<br>> 99.8000        5.04165        0.0109239<br>> 100.0000        5.04156        0.158978<br>> <br>> $ tail force.xvg<br>> 98.2000        70.7804<br>> 98.4000        64.2902<br>> 98.6000        12.6735<br>> 98.8000        -60.3298<br>> 99.0000        -77.457<br>> 99.2000        11.415<br>> 99.4000        85.1327<br>> 99.6000        99.6576<br>> 99.8000        44.5381<br>> 100.0000        -29.4892<br>> <br>> ########################################<br>> <br>> pull_geometry = direction<br>> pull_init1 = -0.1<br>> pull_vec1 = 0 0 1<br>> <br>> $ tail coord.xvg<br>> 98.2000        5.02845        -0.0551189<br>> 98.4000        5.02783        -0.0799781<br>> 98.6000        5.0266        -0.145213<br>> 98.8000        5.02534        -0.112499<br>> 99.0000        5.02392        -0.06543<br>> 99.2000        5.02339        -0.0648827<br>> 99.4000        5.02286        -0.130913<br>> 99.6000        5.02251        -0.196036<br>> 99.8000        5.02211        -0.190228<br>> 100.0000        5.02168        -0.216231<br>> <br>> $ tail force.xvg<br>> 98.2000        -22.4406<br>> 98.4000        -10.0109<br>> 98.6000        22.6063<br>> 98.8000        6.24961<br>> 99.0000        -17.285<br>> 99.2000        -17.5586<br>> 99.4000        15.4567<br>> 99.6000        48.0178<br>> 99.8000        45.1138<br>> 100.0000        58.1155<br>> <br>> ###############################<br>> <br>> pull_geometry = direction<br>> pull_init1 = 0.1<br>> pull_vec1 = 0 0 -1<br>> <br>> $ tail coord.xvg<br>> 98.2000        5.05883        -0.110131<br>> 98.4000        5.05931        -0.156342<br>> 98.6000        5.0597        -0.143227<br>> 98.8000        5.05965        -0.13037<br>> 99.0000        5.05919        -0.0630012<br>> 99.2000        5.06013        -0.0468867<br>> 99.4000        5.06169        -0.1017<br>> 99.6000        5.06282        -0.205357<br>> 99.8000        5.06437        -0.194031<br>> 100.0000        5.06543        -0.139003<br>> <br>> $ tail force.xvg<br>> 98.2000        -5.0653<br>> 98.4000        -28.1712<br>> 98.6000        -21.6133<br>> 98.8000        -15.1848<br>> 99.0000        18.4994<br>> 99.2000        26.5566<br>> 99.4000        -0.850237<br>> 99.6000        -52.6784<br>> 99.8000        -47.0155<br>> 100.0000        -19.5014<br>> <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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