Hi Gromacs Friends,<br>Thank you for your reply and nice suggestion.<br>I read the wikipedia article ..<a href="http://en.wikipedia.org/wiki/Flying_ice_cube" target="_blank">http://en.wikipedia.org/wiki/Flying_ice_cube</a><span class="HOEnZb"><font color="#888888"> suggested by Mark..<br>
<br></font></span>as per the article.. <br>More conservatively, the rate of velocity rescaling can be reduced,
the scale factor computed over a time-averaged sample of instantaneous
temperatures, or an alternative means of thermostatting such as the <a href="http://en.wikipedia.org/wiki/Nos%C3%A9-Hoover_thermostat" title="Nosé-Hoover thermostat" class="mw-redirect">Nosé-Hoover thermostat</a> can be used.<br>
<br>So I used the Nose-Hover thermostat..<br>after finished mdrun , to see movie I used the command trjconv -s ..tpr -f ...xtc -pbc nojump -o protein.pdb -dt 10 -center <br>I found that after these command also my molecule some time moving the out of box ..Is it right???<br>
<br> In these MD run I not remove COM(center of motion) so I want to check it is <br>not producing any misleading and run is not wrong (No flying ice cube effect)..??<br><br> the grommp warning was like ..<br><br>WARNING 1 [file md.mdp]:<br>
You are not using center of mass motion removal (mdp option comm-mode),<br>
numerical rounding errors can lead to build up of kinetic energy of the<br>
center of mass<br> And I used Maxwarn 1... So Now I want to check is these warning <br>affect my run ...which proparty I have to check ??<br>Thank you in advance..<br><br><div class="gmail_quote">On Sat, Mar 24, 2012 at 9:41 PM, 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 class="im">On 24/03/2012 11:06 PM, rama david wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Gromacs Specialist,<br>
I want to study How the protein interact<br>
with each other ??<br>
</blockquote>
<br></div>
Great, but whether or not you remove center of mass translation *of the whole system* has nothing directly to do with it.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I run one simulation with following MDP file option ..<br>
comm_mode = Linear ; remove center of mass translation<br>
nstcomm = 1 ; [steps] frequency of mass motion removal<br>
comm_grps = Protein Non-Protein ; group(s) for center of mass motion removal<br>
<br>
<br>
Now I decided to remove the center of mass<br>
with following option .........<br>
</blockquote>
<br></div>
Changing this option to "None" doesn't "remove the center of mass", it stops removing the motion of the center of mass.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
comm_mode = None ; remove center of mass translation<br>
nstcomm = ; [steps] frequency of mass motion removal<br>
comm_grps = ; group(s) for center of mass motion removal<br>
<br>
I got the following warning at the command grompp...<br>
<br>
WARNING 1 [file md.mdp]:<br>
You are not using center of mass motion removal (mdp option comm-mode),<br>
numerical rounding errors can lead to build up of kinetic energy of the<br>
center of mass<br>
<br>
I run with maxwarn 1 , Is I am right??<br>
</blockquote>
<br></div>
Do you know why you can ignore this warning? If not, do not use -maxwarn.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
What Is reason for above error??<br>
</blockquote>
<br></div>
You're getting a warning because you are doing something that might be wrong - in fact, likely to be wrong. See <a href="http://en.wikipedia.org/wiki/Flying_ice_cube" target="_blank">http://en.wikipedia.org/wiki/<u></u>Flying_ice_cube</a><span class="HOEnZb"><font color="#888888"><br>
<br>
Mark<br>
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</font></span></blockquote></div><br>