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<div class=Section1><pre><font size=2 face="Courier New"><span lang=EN-US
style='font-size:10.0pt'>Dear Gromacs-users and developers,</span></font></pre><pre><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt'> </span></font></pre><pre><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt'>I use GROMACS for studying the hydrotation free energy of alkane molecules </span></font></pre><pre><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt'>using the free energy perturbation method. Thereto I calculated trajectory </span></font></pre><pre><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt'>and energy for </span></font><font
color=black face=Symbol><span lang=EN-US style='font-family:Symbol;color:black'>l</span></font><font
color=black><span lang=EN-US style='color:black'>=</span></font><font
color=black face=Symbol><span lang=EN-US style='font-family:Symbol;color:black'>l</span></font><sub><font
color=black><span lang=EN-US style='color:black'>0</span></font></sub><font
color=black><span lang=EN-US style='color:black'> (as an example for </span></font><font
color=black face=Symbol><span lang=EN-US style='font-family:Symbol;color:black'>l</span></font><font
color=black><span lang=EN-US style='color:black'>=0.8) </span></font></pre><pre><font
size=2 color=black face="Courier New"><span lang=EN-US style='font-size:10.0pt;
color:black'>and </span></font><span lang=EN-US>energy for </span><font
color=black face=Symbol><span lang=EN-US style='font-family:Symbol;color:black'>l</span></font><font
color=black><span lang=EN-US style='color:black'>=0.6, </span></font><font
color=black face=Symbol><span lang=EN-US style='font-family:Symbol;color:black'>l</span></font><font
color=black><span lang=EN-US style='color:black'>=0.4, </span></font><font
color=black face=Symbol><span lang=EN-US style='font-family:Symbol;color:black'>l</span></font><font
color=black><span lang=EN-US style='color:black'>=0.2 using programs:</span></font></pre><pre><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt'> </span></font></pre>
<p class=MsoNormal><b><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-weight:bold'>mdrun -s Eth_for_md.tpr -o
Eth_08_traject.trr -c Eth_after_08md.gro -v -e Eth_08_energy.edr </span></font></b></p>
<pre><b><font size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt;
font-weight:bold'> </span></font></b></pre>
<p class=MsoNormal><b><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-weight:bold'>mdrun -rerun Eth_08_traject.trr -s
Eth_for_md.tpr -c Eth_after_08md.gro -v -e </span></font></b></p>
<pre><font size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt'> </span></font></pre><pre><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt'>However, the values “Coulomb-14”, <font
color=black><span style='color:black'>“Coulomb (SR)” and “Coulomb (LR)” for all </span></font></span></font><font
color=black face=Symbol><span lang=EN-US style='font-family:Symbol;color:black'>l¹</span></font><font
color=black><span lang=EN-US style='color:black'>0.8 were the same (and differed from the values for </span></font><font
color=black face=Symbol><span lang=EN-US style='font-family:Symbol;color:black'>l</span></font><font
color=black><span lang=EN-US style='color:black'>=0.8). Furthermore, the values “Box-X, “Box-Y” and “Box-Z” for the cases </span></font><font
color=black face=Symbol><span lang=EN-US style='font-family:Symbol;color:black'>l¹</span></font><font
color=black><span lang=EN-US style='color:black'>0.8 increased.</span></font></pre><pre><font
size=2 color=black face="Courier New"><span lang=EN-US style='font-size:10.0pt;
color:black'> </span></font></pre><pre><font size=2 color=black
face="Courier New"><span lang=EN-US style='font-size:10.0pt;color:black'>What does it mean?</span></font></pre><pre><font
size=2 color=black face="Courier New"><span lang=EN-US style='font-size:10.0pt;
color:black'> </span></font></pre>
<p class=MsoNormal><font size=2 color=black face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";color:black'>Topology
file of C<sub>2</sub></span></font><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New";color:black'>î</span></font><sub><font
size=2 color=black face="Courier New"><span lang=EN-US style='font-size:10.0pt;
font-family:"Courier New";color:black'>6</span></font></sub><font size=2
color=black face="Courier New"><span lang=EN-US style='font-size:10.0pt;
font-family:"Courier New";color:black'> was:</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt'> </span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt'>[ moleculetype ]</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt'>Eth 3</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt'> [ atoms ]</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt'> ; nr type resnr resid
atom cgnr charge
mass typeB
chargeB massB</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt'> 1 opls_135 1
C2 C1 1
-0.180 12.011 opls_135
0.000 12.011</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt'> 2 opls_140 1 C2
H11 1 0.060
1.008
opls_140 0.000 1.008</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt'> 3 opls_140 1
C2 H12 1
0.060 1.008
opls_140 0.000 1.008</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt'> 4 opls_140 1 C2
H13 1
0.060 1.008
opls_140 0.000 1.008</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt'> 5 opls_135 1
C2 C2 1
-0.180 12.011 opls_135
0.000 2.011</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt'> 6 opls_140 1
C2 H21 1
0.060 1.008
opls_140 0.000 1.008</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt'> 7 opls_140 1
C2 H22 1
0.060 1.008
opls_140 0.000 1.008</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt'> 8 opls_140 1
C2 H23 1
0.060 1.008
opls_140 0.000 1.008</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt'> [ bonds ]</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt'> 1 2</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt'>……………………………………………………</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt'>………………………………………………………</span></font></p>
<pre><font size=2 color=black face="Courier New"><span lang=EN-US
style='font-size:10.0pt;color:black'> </span></font></pre><pre><font
size=2 color=black face="Courier New"><span lang=EN-US style='font-size:10.0pt;
color:black'>And the second question. </span></font></pre><pre><font size=2
color=black face="Courier New"><span lang=EN-US style='font-size:10.0pt;
color:black'>There are two unintelligible strings in the heading of file runavgdf.xvg (result of the program </span></font><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt;
font-family:"Times New Roman"'>g_energy</span></font><span lang=EN-US> with option –f2):</span></pre><pre><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt'> </span></font></pre>
<p class=MsoNormal><b><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt;font-weight:bold'>@ view 0.15, 0.15, 0.75, 0.85 </span></font></b></p>
<pre><b><font size=3 face="Times New Roman"><span lang=EN-US style='font-size:
12.0pt;font-family:"Times New Roman";font-weight:bold'>@ legend 0.78, 0.8 </span></font></b></pre><pre><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt'> </span></font></pre><pre><font
size=2 color=black face="Courier New"><span lang=EN-US style='font-size:10.0pt;
color:black'>What does its mean?</span></font></pre>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt'> </span></font></p>
<pre><font size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt'> </span></font></pre><pre><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt'>Thank you in advance,</span></font></pre><pre><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt'> </span></font></pre><pre><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt'>Mikhail Mazo</span></font></pre><pre><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt'> </span></font></pre><pre><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt'>Dr. M. Mazo</span></font></pre><pre><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt'>Computer Simulation Group</span></font></pre>
<p class=MsoBodyText><font size=2 color=black face="Courier New"><span
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";color:black;
layout-grid-mode:line'>Department of polymers and composites</span></font></p>
<pre><font size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt'>Institute</span></font><span
lang=EN-US> of </span><span lang=EN-US>Chemical</span><span lang=EN-US> Physics </span></pre><pre><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt'>Kosygina 4, </span></font><span
lang=EN-US>Moscow</span></pre><pre><font size=2 face="Courier New"><span
lang=EN-US style='font-size:10.0pt'>119991, </span></font><span lang=EN-US>Russia</span><span
lang=EN-US> </span></pre><pre><font size=2 face="Courier New"><span lang=EN-US
style='font-size:10.0pt'>Tel.: 07 (095) 939-7515</span></font></pre><pre><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt'>e-mail: <a
href="mailto:mikhail.mazo@algodign.com">mikhail.mazo@algodign.com</a> </span></font></pre><pre><font
size=2 face="Courier New"><span lang=EN-US style='font-size:10.0pt'> </span></font></pre>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'> </span></font></p>
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