Thanks Mark. I looked at the link you has sent. However, with pressure coupling I haven't seen such fluctuations for my system. The pressure value is the one obtained at the end of a long NPT simulation - 10^8 steps with dt=10^-4. The rms fluctuations in pressure are small, of the order of 1-0.1 bar. <div>
<br><br><div class="gmail_quote">On Tue, Jun 8, 2010 at 6:34 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">----- Original Message -----<br>From: Sai Pooja <<a href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a>><br>Date: Wednesday, June 9, 2010 8:07<br>Subject: [gmx-users] Reduced LJ Units<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br><br><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font>Hi,<div>
<br></div><div><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font>I have trouble searching mailing lists so I apologize if this has already been answered in some query.</div>
<div><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font><br></div><div><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font>If sigma=epsilon=mass=1 is specified in .top file then for specifying T*=1 in the Thermostat does one need to set ref_t ~ 120 ?</div>
<div><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font><br></div><div><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font>Similarly, to specify ref_p for the Barostat, is there a similar conversion factor?</div>
<div><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font><br></div></div><div><div class="im"><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font>How about the values of P reported in bar? How does one convert that to reduced units?<br>
<br></div>Does manual table 2.4 help?<div class="im"><br><br clear="all"><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font>I ask this because I have currently specified ref_t =120 as explained in the Gromacs manual. However this gives me a pressure value(in bars) which is much much larger than the one I had expected in reduced units (by a factor of about 50-60).</div>
</div><br>Are you measuring pressure over long enough time? See <a href="http://www.gromacs.org/Documentation/Terminology/Pressure" target="_blank">http://www.gromacs.org/Documentation/Terminology/Pressure</a><br><font color="#888888"><br>
Mark
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