<div dir="ltr">Hi Mark,<br><br>Thank you for the reply. I decided to just test my own simple SD integrator. After calling do_force() I update the positions. Example:<br><br>int i = 0, dim = 3;<br>real sd_step_size = 0.01;<br><br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">for(i = 0; i < mdatoms->nr; i++)<br> for(d = 0; d < dim; d++) {<br> state->x[i][d] += sd_step_size * f[i][d];</blockquote><div><br>The code *works* , but the output doesnt make much sense. When I print the force (f[i][d]), I get a lot of zeros. Am I doing this right? I'm afraid I might not be accessing the forces (stored locally on each processor) correctly. Any suggestions?<br><br>Thanks!</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr"><div><font face="georgia, serif"> <br></font><font color="#888888"><span style="font-size:13px;background-color:rgb(255,255,255)"><div style="font-family:arial,sans-serif"><b style="color:rgb(7,55,99);font-family:'trebuchet ms',sans-serif;font-size:small">Andrew Abi-Mansour</b><font face="georgia, serif"><br></font></div></span></font></div></div></div></div>
<br><div class="gmail_quote">On Sat, Feb 7, 2015 at 6:54 AM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi,<div><br></div><div>Probably you are over- or under-managing periodic boundaries and/or domain decomposition. I would think you should refactor out of do_steep exactly the part you need, since it's not designed to be a callable utility routine. For example, you probably don't want it to ever call em_dd_partition_system()...</div><div><br></div><div>Mark</div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="h5">On Sat, Feb 7, 2015 at 7:15 AM, Andrew AbiMansour <span dir="ltr"><<a href="mailto:anabiman@umail.iu.edu" target="_blank">anabiman@umail.iu.edu</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div dir="ltr"><span style="font-size:12.7272720336914px">Hi,</span><br style="font-size:12.7272720336914px"><br style="font-size:12.7272720336914px"><span style="font-size:12.7272720336914px">I would like to call the integrator function do_steep() from within do_md(). I modified some constraints parameters in t_inputrec before passing all the arguments supplied to do_md() by the user to do_steep(). This simple approach, however, does not work and GROMACS crashes complaining about a charge group moving too far. The coordinates seem to change by several nano meters over a single SD step. What is this happening? and Do you have any suggestions on how to implement this right?</span><br style="font-size:12.7272720336914px"><br style="font-size:12.7272720336914px"><span style="font-size:12.7272720336914px">Thanks</span><br clear="all"><div><div><div dir="ltr"><div><font face="georgia, serif"> <br></font><font color="#888888"><span style="font-size:13px;background-color:rgb(255,255,255)"><div style="font-family:arial,sans-serif"><b style="color:rgb(7,55,99);font-family:'trebuchet ms',sans-serif;font-size:small">Andrew Abi-Mansour</b><font face="georgia, serif"><br></font></div></span></font></div></div></div></div>
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