<font color="#000099">Yes, the water certainly drifts along with the membrane. Umm, it is safe to remove the COM momentum in an NPT (Langevin+piston) simulation?<br><br>Later I want to do a steered dynamics simulation for this system. The external applied force will certainly produce a nonzero net momentum. Is it safe to remove the COM momentum in this case?<br>
<br>-Jose<br clear="all"></font><span style="color:rgb(0,0,153)"></span><br><br><div class="gmail_quote">On Thu, Feb 23, 2012 at 8:35 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"><div class="im">
On 23/02/2012 10:27 PM, Jose Borreguero wrote:
<blockquote type="cite"><font color="#000099">I am not referring to any drift
of the whole system, but to the diffusion of the lipid bilayer
only. Diffusion of molecules in water is to be expected given
sufficient time. I wonder what is a reasonable restraint to keep
the center of mass of the membrane at Z=0.0<br>
</font></blockquote>
<br></div>
You can't have the bilayer drift unless the water drifts with it or
through it. The former is more likely, thus you likely have COM
motion.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span><div class="im"><br>
<br>
<blockquote type="cite"><font color="#000099">
<br>
</font><span style="color:rgb(0,0,153)">-Jose</span><br>
<br>
<div class="gmail_quote">On Wed, Feb 22, 2012 at 9:04 PM, Mark
Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>
<div> On 23/02/2012 10:26 AM, Jose Borreguero
wrote:
<blockquote type="cite">
<div class="gmail_quote"><font color="#000099">Dear
GROMACS users,<br>
<br>
While simulating a DLPC membrane, I noticed that
it tends to diffuse along the normal (Z-axis)
component. Is there a 'standard' restrain that is
used to prevent such diffusion?<br>
The first option I thought was to restrain the
center of mass of the whole membrane along the
Z-axis, but I don't know what is a reasonable
value for the force constant.<br>
If anyone has any experience dealing with this
kind of problem, please do reply.</font><br>
</div>
</blockquote>
</div>
</div>
<font color="#000099"><br>
Diffusion of the center of mass of the whole system is
something that can be removed by an existing mechanism.
See manual 7.3.3<span><font color="#888888"><br>
<br>
Mark<br>
</font></span></font> </div>
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