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Hi,<br><br>If you read the manual carefully, you would have noticed that the potential<br>is interpolated using cubic spline interpolation and the forces are the derivative<br>of these splines. Your scheme would work if the forces would be interpolated linearly.<br><br>Berk<br><br>> From: junsookim76@gmail.com<br>> To: gmx-users@gromacs.org<br>> Date: Thu, 11 Mar 2010 10:55:03 -0500<br>> Subject: [gmx-users] Brownian Dynamics - Tabulated Potential<br>> <br>> Hi,<br>> <br>> I am trying the brownian dynamics simulations of a polymer chain using <br>> FENE potential and some effective potential. For this purpose, I made <br>> tabulated potentials for polymer bonds and non-bonded interactions, <br>> and the simulations are running fine.<br>> <br>> As far as I know, the Brownian dynamics simulations only need the <br>> forces at each time step (eq. 3.64 in Manual). So I tested the BD <br>> simulation by setting the potential energy equal to Zero while keeping <br>> the force unchanged. Then I have a problem with simulations. The bonds <br>> are broken. I do not understand why we need the potential energy in <br>> Brownian dynamics simulations. It would be really appreciated if <br>> anyone provides any hint.<br>> <br>> Here is a piece of the bonding tabulated potential of FENE with the <br>> potential set as zero and the force unchanged.<br>> <br>> Thanks,<br>> Jun Soo<br>> <br>> # r U(r) -U'(r) <br>> 4.950 0.00000 11.5494<br>> 4.952 0.00000 9.29470<br>> 4.954 0.00000 7.10307<br>> 4.956 0.00000 4.97242<br>> 4.958 0.00000 2.90067<br>> 4.960 0.00000 0.885859<br>> 4.962 0.00000 -1.07395<br>> 4.964 0.00000 -2.98060<br>> 4.966 0.00000 -4.83590<br>> 4.968 0.00000 -6.64158<br>> 4.970 0.00000 -8.39931<br>> 4.972 0.00000 -10.1107<br>> 4.974 0.00000 -11.7774<br>> 4.976 0.00000 -13.4008<br>> 4.978 0.00000 -14.9825<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 />New Windows 7: Find the right PC for you. <a href='http://windows.microsoft.com/shop' target='_new'>Learn more.</a></body>
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