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Hi,<br><br>pullx.xvg has the coordinates of group 0 and the distances<br>of the other groups to group 0.<br><br>pullf.xvg has the force of the umbrella potential<br>which works along the direction vector you gave,<br>this can be positive or negative depending on the direction.<br><br>Berk<br><br>> Subject: RE: [gmx-users] Pull Code problems<br>> From: genesup@gmail.com<br>> To: gmx-users@gromacs.org<br>> Date: Tue, 13 Jan 2009 18:02:47 +0300<br>> <br>> OK, <br>> I did some homework and now I`m up to this:<br>> <br>> ;-----------PULL CODE ---------------------<br>> <br>> pull = umbrella<br>> pull_geometry = direction<br>> pull_group0 = r_500<br>> pull_group1 = r_535<br>> pull_vec1 = -1.306 1.355 -0.319<br>> pull_k1 = 1000<br>> pull_rate1 = 0.5 ; nm/ps Extreme parameters for extreme pulling<br>> <br>> Now I have two output files - pullx.xvg (-px option of mdrun) and<br>> pullf.xvg (-pf option).<br>> <br>> pullx :<br>> <br>> @ title "Pull COM"<br>> @ xaxis label "Time (ps)"<br>> @ yaxis label "Position (nm)"<br>> @TYPE xy<br>> @ view 0.15, 0.15, 0.75, 0.85<br>> @ legend on<br>> @ legend box on<br>> @ legend loctype view<br>> @ legend 0.78, 0.8<br>> @ legend length 2<br>> @ s0 legend "0 X"<br>> @ s1 legend "0 Y"<br>> @ s2 legend "0 Z"<br>> @ s3 legend "1 dX"<br>> @ s4 legend "1 dY"<br>> @ s5 legend "1 dZ"<br>> 0.000000 3.899593 5.816368 3.246447<br>> -0.285972 -0.132647 -0.183023<br>> 0.040000 3.901163 5.812132 3.238992<br>> -0.292108 -0.141616 -0.180796<br>> 0.080000 3.902505 5.806212 3.240236<br>> -0.314770 -0.143951 -0.186194<br>> 0.120000 3.905365 5.797938 3.242384<br>> -0.336802 -0.142276 -0.197704<br>> 0.160000 3.908899 5.794812 3.230687<br>> -0.342824 -0.160593 -0.178745<br>> 0.200000 3.910108 5.797564 3.220754<br>> -0.340151 -0.161146 -0.152076<br>> <br>> Am I correct about XYZ being position of the spring and dx dy dz -<br>> group0-group1 distances?<br>> <br>> pullf :<br>> <br>> @ title "Pull force"<br>> @ xaxis label "Time (ps)"<br>> @ yaxis label "Force (kJ/mol/nm)"<br>> @TYPE xy<br>> 0.000000 -132.088161<br>> 0.004000 -128.605515<br>> 0.008000 -125.008520<br>> 0.012000 -121.568624<br>> 0.016000 -118.475655<br>> 0.020000 -115.844403<br>> 0.024000 -113.735184<br>> 0.028000 -112.165522<br>> 0.032000 -111.066433<br>> ..... .......<br>> 1.232000 409.573773<br>> 1.236000 412.738957<br>> 1.240000 415.736038<br>> 1.244000 418.446270<br>> 1.248000 420.781766<br>> 1.252000 422.747570<br>> 1.256000 424.505472<br>> 1.260000 426.348269<br>> 1.264000 428.568933<br>> 1.268000 431.301610<br>> 1.272000 434.467394<br>> <br>> Why does it start with negative values? Should I use negative value for<br>> pull_k1 (force constant)?<br>> <br>> Thank you for your answers, I appreciate your time.<br>> <br>> SDA<br>> <br>> <br>> <br>> On Tue, 2009-01-13 at 12:41 +0100, Berk Hess wrote:<br>> > Hi,<br>> > <br>> > You don't indicate which xvg file was 0, I guess pullf.xvg.<br>> > Could it be that you did not specify a force constant, meaning fc=0?<br>> > <br>> > Berk<br>> > <br>> > > From: genesup@gmail.com<br>> > > To: gmx-users@gromacs.org<br>> > > Date: Tue, 13 Jan 2009 14:26:47 +0300<br>> > > Subject: [gmx-users] Pull Code problems<br>> > > <br>> > > Hello,<br>> > > <br>> > > I am trying to run a pulling simulation with gromacs 4.0.2.<br>> > > <br>> > > I have appended the following pull code to the mdp file:<br>> > > <br>> > > ;-----------PULL CODE ---------------------<br>> > > <br>> > > pull = umbrella<br>> > > pull_geometry = direction<br>> > > pull_group0 = r_500<br>> > > pull_group1 = r_535<br>> > > pull_vec1 = -1.306 1.355 -0.319<br>> > > <br>> > > Where r_500 is the group I am expecting to be pulled,<br>> > > r_535 - the reference (the acid that is in fact in contact with<br>> > > r_500)<br>> > > <br>> > > I have left all remaining parameters with default values. <br>> > > <br>> > > The problem is that NOTHING HAPPENED! XVG file had 0.0000 throughout<br>> > > simulation indicating that distance between pull group and reference<br>> > > group was 0! <br>> > > <br>> > > 1/ What did I do wrong?<br>> > > 2/ Is there any pull code tutorial for gromacs 4 (not previous<br>> > > version)? <br>> > > <br>> > > Thank you!<br>> > > SDA<br>> > > <br>> > > _______________________________________________<br>> > > gmx-users mailing list gmx-users@gromacs.org<br>> > > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > > Please search the archive at http://www.gromacs.org/search before<br>> > 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>> > <br>> > ______________________________________________________________________<br>> > What can you do with the new Windows Live? Find out<br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.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 />What can you do with the new Windows Live? <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>Find out</a></body>
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