Hello David,<br><br>Thanks a lot for your response. My major concern is that this statement does not show up as often in most of the simulations but in some it shows up like illustrated below* (continuously). For example, it does not show up in protein+water simulations but does comes up in ion+water simulations continuously (both are NPT simulations therefore the box volume fluctuates in both cases)<br>
<pre><tt><tt><tt><tt>*Grid: 5 x 5 x 5 cells<br>Grid: 4 x 4 x 4 cells<br>Grid: 5 x 5 x 5 cells<br>Grid: 4 x 4 x 4 cells<br>Grid: 5 x 5 x 5 cells<br>Grid: 4 x 4 x 4 cells<br></tt></tt></tt></tt></pre><br> Is there a particular reason for this? From my observation, it appears that the frequency of this statement is independent of the frequency with which the md.log is written. <br>
<br>Thank you<br><br>Regards<br>Sapna<br><br><div class="gmail_quote">On Thu, May 29, 2008 at 4:45 PM, sapna sarupria <<a href="mailto:sapna.sarupria@gmail.com">sapna.sarupria@gmail.com</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div></div><div class="Wj3C7c"><pre><tt><tt>Dear All,<br><br> During simulations of some ions solvated in water<br>(where water is constrained using SHAKE) I get the<br>statements looking like the following in the md.log<br>
files:<br>Grid: 4 x 4 x 4 cells<br>
Grid: 5 x 5 x 5 cells<br>Grid: 4 x 4 x 4 cells<br>Grid: 5 x 5 x 5 cells<br>Grid: 4 x 4 x 4 cells<br>Grid: 5 x 5 x 5 cells<br>Grid: 4 x 4 x 4 cells<br><br>The system consists of 10 ion pairs and water (SPC/E,<br>518 water molecules) and simulations are run in NPT<br>
ensemble (T=280 K). Can anyone please explain what<br>this statement means and if it should be a cause of<br>concern. The simulations have run without crashing for<br>25 ns. The simulations were run using gromacs 3.2.<br>
Similar output was found in gromacs 3.3 simulations<br>except in this case there is only one ion pair (in 518<br>water molecules) which is constrained at a certain<br>distance using constraint = all_bonds in run.mdp file.<br>
<br>Thanks in advance for your response.<br><br>Regards<br>Sapna <br><br><br></tt></tt></pre><br clear="all"><br></div></div>-- <br>Sapna Sarupria<br>Ph.D. Student - Chemical Engineering<br>Rensselaer Polytechnic Institute<br>
Troy, New York 12180<br>
U.S.A.<br>Ph#: (518)276-3031<br>Life isn't about finding yourself. Life is about creating yourself. <br>George Bernard Shaw. <br>Dare to Dream
</blockquote></div><br><br clear="all"><br>-- <br>Sapna Sarupria<br>Ph.D. Student - Chemical Engineering<br>Rensselaer Polytechnic Institute<br>Troy, New York 12180<br>U.S.A.<br>Ph#: (518)276-3031<br>Life isn't about finding yourself. Life is about creating yourself. <br>
George Bernard Shaw. <br>Dare to Dream