<div>Thank Apoorv and David,</div>
<div> </div>
<div>If the GMX can use the volecities of y-axis and z-axis, it will overcome this question.</div>
<div> </div>
<div>However, it seems that the question was not resolved on the basis of David.</div>
<div> </div>
<div>Any other people give some advice? </div>
<div> </div>
<div>Thanks very much.<br><br></div>
<div class="gmail_quote">2011/4/23 David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>></span><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im">On 2011-04-23 09.38, Apoorv Kalyankar wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">In GROMACS, I believe that whenever an external force is applied, the<br>mean velocity of the group is subtracted before rescaling the<br>
velocities and then the mean velocity is added back in. So if you are<br>expecting a plug like flow then there should not be any problem. In<br>other cases also, it should not create a problem since your external<br>electric field is not that large.<br>
<br></blockquote></div>This is correct for the acceleration option, but not for the electric field. Hence the E-field will introduce friction that will heat up the system.
<div class="im"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">And yes you should not remove the center of mass motion of the<br>molecules otherwise you will get zero velocity.<br>
</blockquote></div>Correct.
<div class="im"><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br>Apoorv<br><br>On Fri, Apr 22, 2011 at 2:09 AM, lammps lammps<<a href="mailto:lammp2forum@gmail.com" target="_blank">lammp2forum@gmail.com</a>> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi,<br><br>I want to use the option of E_x = 1 0.01 0 to add an electric field to<br>the simulated system in NVT ensemble.<br>
<br>Because there should exist an no zero velocity of center-of-mass in the x<br>direction. It seems that it is wrong to directly use the nose-hoover to<br>control the temperature.<br><br>it is also not reasonable to use nstcomm = 1, because the velocity of<br>
center-of mass in the x-axis should be kept when runing.<br><br>So, How to control the temperature? When calcating the temperature in the<br>process of simulations, how to exclude the velocity of center-of-mass of x<br>direction for controling the right T?<br>
<br>Thanks in advance.<br><br>--<br>wade<br><br>--<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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<br></blockquote></blockquote><br><br>-- <br></div>David van der Spoel, Ph.D., Professor of Biology<br>Dept. of Cell & Molec. Biol., Uppsala University.<br>Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br><a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se/" target="_blank">http://folding.bmc.uu.se</a><br>
<font color="#888888">-- <br></font>
<div>
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Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
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