<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><h1><span class="Apple-style-span" style="font-size: 12px; font-weight: normal; white-space: pre; ">Dear Erik,</span></h1><h1><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; font-weight: normal;">Thank you so much for your prompt reply. I appreciate it.</span></font></h1><h1><span class="Apple-style-span" style="font-size: medium; font-weight: normal; font-family: monospace; white-space: pre; ">Yun-an Yan</span></h1><h1><span class="Apple-style-span" style="font-size: medium; font-weight: normal; font-family: monospace; white-space: pre; ">Erik Marklund writes:</span></h1><h1><span class="Apple-style-span" style="font-size: medium; font-weight: normal; font-family: monospace; white-space: pre; ">>For more exotic NVE-systems I had to do some or several of the following </span></h1><h1><span class="Apple-style-span" style="font-size: medium; font-weight: normal; font-family: monospace; white-space: pre; ">>things to get stable Etot:</span></h1><pre>>* have an even shorter timestep than one would expect from the applied
>constraints and such.
<br></pre><pre>I will try a timestep with 0.5 fs.</pre><pre>>* use double precision.</pre><pre>The double precision is already in use.</pre><pre>>* apply the constraints with lower tolerance/more iterations etc.
</pre><pre>I thought shake_tol = 1.e-8 is small enough. May I try an even smaller value?</pre><pre>Or the lincs algorithm with lincs_order=8 and lincs_iter=2 is recommended </pre><pre>instead of shake?</pre><pre>>Then there's a few things I notice in your setup:
>* I see that you do not use constrints at all. I would give it a shot.</pre><pre>I will try.</pre><pre>
>* Why do you have two separate comm-grps?</pre><pre>Since it is a solute-solvent fashion MD, I am trying to keeping the solute</pre><pre>part close the center of the simulation box. But it does not work in this way.</pre><pre>Do you have any idea about that?
<br></pre><pre>>Erik Marklund
>
>--
>-----------------------------------------------
>Erik Marklund, PhD student
>Dept. of Cell and Molecular Biology, Uppsala University.
>Husargatan 3, Box 596, 75124 Uppsala, Sweden
>phone: +46 18 471 4537 fax: +46 18 511 755
><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">erikm at xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se/</a>
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