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<DIV><FONT face=Arial size=2><SPAN
class=583491706-10012007>Hi,</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=583491706-10012007></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=583491706-10012007>Nobody implied me
till now. So that means the current version can not do BD by implicitly treating
water into continuum media, i.e, use of dielectric constant of water.
</SPAN></FONT><FONT face=Arial size=2><SPAN class=583491706-10012007>I hope Gmx
developers can help me to make sure this. Till to now I am been using Gmx and in
the near future I need to do BD for longer time scale. If Gmx can not help,
it will be bad.</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=583491706-10012007></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=583491706-10012007>thanks in
advance,</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=583491706-10012007></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN
class=583491706-10012007>Zhongqiao</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=583491706-10012007></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN
class=583491706-10012007></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2>Message: 1<BR>Date: Mon, 8 Jan 2007 18:15:10
+0800<BR>From: "Hu Zhongqiao" <<A
href="mailto:zhongqiao_hu@nus.edu.sg">zhongqiao_hu@nus.edu.sg</A>><BR>Subject:
[gmx-users] Can I run BD in water media using Gmx?<BR>To: <<A
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>><BR>Message-ID:<BR> <<A
href="mailto:62AAE6335EB82749B7D92E1DFB8B57848BBA44@MBX21.stu.nus.edu.sg">62AAE6335EB82749B7D92E1DFB8B57848BBA44@MBX21.stu.nus.edu.sg</A>><BR>Content-Type:
text/plain; charset="us-ascii"</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>Dear users,<BR> <BR>I wonder if I can run
Brownian Dynamics in water media using Gmx.<BR>Although I know we can set
integrator=bd, I dont know how to set dielectric constant of water in Gmx
parameter file. Anyone could give some hints for this?
thanks<BR> <BR>Zhongqiao Hu<BR></FONT></DIV>
<DIV> </DIV>
<DIV align=left>
<DIV align=left><FONT face="Times New Roman" size=4>Zhongqiao Hu</FONT></DIV>
<DIV align=left><FONT face="Times New Roman"></FONT> </DIV>
<DIV align=left><FONT face="Times New Roman">Lab E5-04-27</FONT></DIV>
<DIV align=left>
<DIV align=left><FONT face="Times New Roman">Tel: 65161946(O)</FONT></DIV></DIV>
<DIV align=left><FONT face="Times New Roman">Department of Chemical and
Biomolecular Engineering</FONT></DIV>
<DIV align=left><FONT face="Times New Roman">National University of
Singapore</FONT></DIV>
<DIV align=left><FONT face="Times New Roman">117576, Singapore</FONT></DIV>
<DIV align=left><FONT face="Times New Roman"></FONT> </DIV></DIV>
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