<p dir="ltr">Hi,</p>
<p dir="ltr">This would be a good question for the user's mailing list, since it doesn't pertain to the code development. Please continue there. </p>
<p dir="ltr">I suggest you look at the change in energy when you release position restraints after a run that wasn't heated. Why shouldn't there be a drop in energy when you change the Hamiltonian? </p>
<p dir="ltr">Mark</p>
<br><div class="gmail_quote"><div dir="ltr">On Thu, 1 Jun 2017 23:19 Felix Y Yang <<a href="mailto:fyy001@ucsd.edu">fyy001@ucsd.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div id="m_-5821446030496735160divtagdefaultwrapper" style="font-size:12pt;color:#000000;font-family:Calibri,Arial,Helvetica,sans-serif" dir="ltr">
<p><span style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">Hi all,</span><br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">
<br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">
<br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">
<span style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">So I've been trying a series of runs of heating-active-site-of-protein, then NVE, then heating
again, and NVE again. And I've seemed to notice that the total energy of the system between the end of the heating process and the beginning of a NVE step right after it is significantly different, namely dropping a lot in total energy. The total energy seems
to be retained a lot better between the end of an NVE step and the beginning of the next heating step.</span><br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">
<br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">
<br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">
<span style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">Does anyone know what might be the cause of this? I have the protein position-restrained during
the heating step, and released during the NVE step. The heating step is 3 ps, the NVE is 1 ns. For the heating step, I grouped the active site of the protein separately in an index file, and heated only that group, while the rest of the protein has the thermostat
turned off. The other parameters in my mdp file are almost exactly the same for the heating and NVE processes.</span><br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">
<br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">
<br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">
<span style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">Any feedback would be appreciated.</span><br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">
<br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">
<br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">
<span style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">Thanks,</span><br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">
<br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">
<br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">
<span style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">Felix Yang</span><br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">
<br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">
<span style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">Graduate Master's Student</span><br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">
<span style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">Department of Chemistry & Biochemistry</span><br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">
<span style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;font-size:13.3333px">University of California, San Diego</span><br>
</p>
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