<br><br><div class="gmail_quote">On Sat, Oct 8, 2011 at 2:21 AM, Nilesh Dhumal <span dir="ltr"><<a href="mailto:ndhumal@andrew.cmu.edu">ndhumal@andrew.cmu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hello,<br>
<br>
I have a system with 128 emi (cations) and 128 Cl (anions). I run the<br>
simulation for 20 ns.<br>
<br>
I want to save snap-shot at 5ns, 10ns, 15ns and 20ns.<br></blockquote><div>trjconv use -dt 5000 <br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
I don't want to save snap shot for 128 ion-pairs. How can I take average<br>
over 128 ion pairs and save snap shot for a single ion pair.<br></blockquote><div>I don't understand the average mean here? <br>if you wanna get the average.pdb in some time interval try g_rmsf -ox -b -e<br><br>you may wait for some other better answers.<br>
<br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
Basically I want to use classical md geometry for quatum chemical<br>
calculation.<br>
<br>
I am using Gromacs 4.0.7 version.<br>
<br>
Thanks<br>
<br>
Nilesh<br>
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