Hi all,<br><br>I have 2 questions related to the electrostatic energy of the system..<br><br>1) Is <b>total electrostatic energy</b> equal to <b>Coulomb-(SR)</b> <font size="4">+</font> <b>Coul.-recip</b>. OR <b>Coulomb-14</b> <font size="4">+</font> <b>Coulomb-(SR)</b> <font size="4">+</font> <b>Coul.-recip</b>. I am so confused.<br>
<br>I specified in my .mdp file;<br>coulombtype = PME<br>rvdw = 1.0<br>rlist = 1.0<br>rcoulomb = 1.0<br>fourierspacing = 0.16<br>pme_order = 4<br>ewald_rtol = 1e-5<br><br>2) I want to calculate electrostatic interaction energy between 2 residues in my system which has 10 peptides in total. But I think, I should have specified the energy groups composed of that 2 residues in my mdp file before starting the simulation. So in this case, is there any way to get this interaction energy OR can I just calculate the electrostatic energy of the whole system?<br>
<br>Thanks in advance,<br><br>Turgay<br><br><br><br><div class="gmail_quote">2012/6/8 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"><div class="im">
On 8/06/2012 11:51 PM, Turgay Cakmak wrote:
<blockquote type="cite">Thanks Mark.<br>
I want to calculate Coulomb and Lennard-Jones energies using
total_dt100.edr .<br>
But, I am not sure I can get the correct energies?<br>
</blockquote>
<br></div>
Neither am I. Only you know the history of these .edr files.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span><div><div class="h5"><br>
<br>
<blockquote type="cite"><br>
Turgay<br>
<br>
<div class="gmail_quote">2012/6/8 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div> On 8/06/2012 10:40 PM, Turgay Cakmak wrote:
<blockquote type="cite"><br>
Hi all,<br>
<br>
I have encountered a problem using eneconv with -dt
flag.<br>
I have several energy files. Firstly, I concatenated
them using the following.<br>
<br>
<span style="font-size:11.0pt;line-height:115%;font-family:"Calibri","sans-serif"" lang="EN-US">eneconv</span><span style="font-size:11.0pt;line-height:115%;font-family:"Calibri","sans-serif"" lang="EN-US"> <span> </span>-f <span></span>first.edr
second.edr .... -settime <span> </span>-o <span></span>total.edr
</span><br>
<br>
But, total.edr is so large. To reduce the size of file,
I used the below command:<br>
<span style="font-size:11.0pt;line-height:115%;font-family:"Calibri","sans-serif"" lang="EN-US"><br>
eneconv -f total.edr -dt 100 -o total_dt100.edr<span>
</span></span><br>
<br>
But, I get the following warning:<br>
<font size="4"><b> .</b></font><br>
<b> <font size="4">.</font></b><br>
<br>
WARNING: missing energy sums at time 69984.000000<br>
<br>
WARNING: missing energy sums at time 69988.000000<br>
<br>
WARNING: missing energy sums at time 69992.000000<br>
<br>
WARNING: missing energy sums at time 69996.000000<br>
Reading energy frame 35000 time 70000.000 <br>
WARNING: missing energy sums at time 70000.000000<br>
Last energy frame read 35000 time 70000.000 <br>
Last step written from energy.edr: t 70000, step
35000000<br>
<br>
Last frame written was at step at step 35000000, time
70000.000000<br>
Wrote 701 frames<br>
</blockquote>
<br>
</div>
At some point something did something to break the usual
format of the files... but we can have no idea what.
<div><br>
<br>
<blockquote type="cite"><br>
Eventually, I get the "total_dt100.edr". But, I am not
sure I could continue using this file.<br>
If someone could help me, I would be glad.<br>
</blockquote>
<br>
</div>
Depends what you want to use it for.<span><font color="#888888"><br>
</font></span></div>
</blockquote>
<div> </div>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"><span><font color="#888888"> <br>
Mark<br>
</font></span></div>
<br>
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