<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Thank you very much for your reply. It is written in the manual and now I understand why.<div><br></div><div>Thanks,</div><div>Jun Soo</div><div><br><div><div>On Mar 11, 2010, at 11:04 AM, Berk Hess wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div class="hmmessage" style="font-size: 10pt; font-family: Verdana; ">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:<span class="Apple-converted-space"> </span><a href="mailto:junsookim76@gmail.com">junsookim76@gmail.com</a><br>> To:<span class="Apple-converted-space"> </span><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> Date: Thu, 11 Mar 2010 10:55:03 -0500<br>> Subject: [gmx-users] Brownian Dynamics - Tabulated Potential<br>><span class="Apple-converted-space"> </span><br>> Hi,<br>><span class="Apple-converted-space"> </span><br>> I am trying the brownian dynamics simulations of a polymer chain using<span class="Apple-converted-space"> </span><br>> FENE potential and some effective potential. For this purpose, I made<span class="Apple-converted-space"> </span><br>> tabulated potentials for polymer bonds and non-bonded interactions,<span class="Apple-converted-space"> </span><br>> and the simulations are running fine.<br>><span class="Apple-converted-space"> </span><br>> As far as I know, the Brownian dynamics simulations only need the<span class="Apple-converted-space"> </span><br>> forces at each time step (eq. 3.64 in Manual). So I tested the BD<span class="Apple-converted-space"> </span><br>> simulation by setting the potential energy equal to Zero while keeping<span class="Apple-converted-space"> </span><br>> the force unchanged. Then I have a problem with simulations. The bonds<span class="Apple-converted-space"> </span><br>> are broken. I do not understand why we need the potential energy in<span class="Apple-converted-space"> </span><br>> Brownian dynamics simulations. It would be really appreciated if<span class="Apple-converted-space"> </span><br>> anyone provides any hint.<br>><span class="Apple-converted-space"> </span><br>> Here is a piece of the bonding tabulated potential of FENE with the<span class="Apple-converted-space"> </span><br>> potential set as zero and the force unchanged.<br>><span class="Apple-converted-space"> </span><br>> Thanks,<br>> Jun Soo<br>><span class="Apple-converted-space"> </span><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>><span class="Apple-converted-space"> </span><br>> --<span class="Apple-converted-space"> </span><br>> gmx-users mailing list<span class="Apple-converted-space"> </span><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>><span class="Apple-converted-space"> </span><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class="Apple-converted-space"> </span>before posting!<br>> Please don't post (un)subscribe requests to the list. 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Use the<span class="Apple-converted-space"> </span><br>www interface or send it to<span class="Apple-converted-space"> </span><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a></div></span></blockquote></div><br></div></body></html>