Hello Justin,<br><br>I am trying to generate the top file for polyethylene chain using the<br>information from the archive:
<a href="http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html</a>. In the former post you said parameters in the I am referring to are not necessarily correct.<br>
<br>1- By parameters you mean the coordinates in pdb file? The residues in this link seem correct to me but I am not sure if the hdb file is correct. <br><br>2- Could you please tell me how to generate a longer chain with the given residue types proposed in the above post. <br>
<pre>ATOM 1 C1 EthB 1 1.000 1.540 0.000<br>ATOM 2 C2 EthB 1 2.456 2.041 0.000<br>ATOM 3 C1 Eth 2 2.456 3.581 0.000<br>ATOM 4 C2 Eth 2 3.912 4.083 0.000<br>
ATOM 5 C1 EthE 3 3.912 5.623 0.000<br>ATOM 6 C2 EthE 3 5.368 6.124 0.000<br>END<br></pre>
Here I do not see hydrogen atoms. I have created a long chain with 100 monomer units using Ascalaph designer. However the file is not properly formatted. i.e atoms are not numbered and residue name is missing. I do not want to alter the file by hand. Can you guide me how I can build a long chain with the residues you proposed in the above post (including hydrogen atoms)<br>
<br>HETATM 1 C 1 2.739 2.554 -0.012 -0.390 C <br>HETATM 2 H 1 2.736 3.644 -0.012 0.130 H <br>HETATM 3 H 1 2.190 2.217 -0.893 0.130 H <br>
HETATM 4 H 1 2.190 2.217 0.868 0.130 H <br>HETATM 5 C 2 4.155 1.993 -0.012 -0.260 C <br>.<br>.<br>HETATM 291 H 97 72.086 -97.891 -0.012 0.130 H <br>
HETATM 292 H 97 70.558 -97.880 0.869 0.130 H <br>HETATM 293 H 97 70.558 -97.880 -0.893 0.130 H <br><br>3- I have also an inquiry about the density of my solvent. One of the experts told me:<br>
<br>Best thing you can do is, make a NPT simulation (look for the right<br>
compresibility) and look how much your density is off,if it's only a<br>
little your fine.<br><br>I dont realize the statement "look how much your density is off"?<br>The desnity is approx. 71000 Kg/m3 (4molecuels per nm3). From NPT run I see the density is 577 Kg/m3. and the volume is<br>
30 nm3 (values from g_energy). How can I make sure if density changes are reasonable?<br>
<br>
*Volume <b> 30.9568</b> 0.374111 0.204815<br><br>
Density (SI) <b>577.914</b> 6.97804 3.80252<br><br><meta http-equiv="Content-Type" content="text/html; charset=utf-8"><meta name="ProgId" content="Word.Document"><meta name="Generator" content="Microsoft Word 11"><meta name="Originator" content="Microsoft Word 11"><link rel="File-List" href="file:///C:%5CDOCUME%7E1%5Cmoeed%5CLOCALS%7E1%5CTemp%5Cmsohtml1%5C01%5Cclip_filelist.xml"><style>
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<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">Energy<span style=""> </span>Average<span style=""> </span>RMSD<span style="">
</span>Fluct.<span style=""> </span>Drift<span style=""> </span>Tot-Drift</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">-------------------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p><span style="font-size: 11pt; font-family: Arial;"></span>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">Temperature<span style=""> </span>297.366<span style=""> </span>12.086<span style="">
</span>11.4021<span style=""> </span>1.38812<span style=""> </span>13.884</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">Pressure
(bar)<span style=""> </span>-30.0299<span style=""> </span>746.524<span style="">
</span>745.665<span style=""> </span>-12.3992<span style=""> </span>-124.017</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p><span style="font-size: 11pt; font-family: Arial;"></span>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><b><span style="font-size: 11pt; font-family: Arial;">Volume<span style=""> </span>30.9568<span style=""> </span>0.374111<span style="">
</span>0.204815<span style=""> </span>-0.108427<span style=""> </span>-1.08449</span></b></p>
<p class="MsoNormal"><b><span style="font-size: 11pt; font-family: Arial;"></span></b></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"><b>Density
(SI)<span style=""> </span>577.914<span style=""> </span>6.97804<span style="">
</span>3.80252<span style=""> </span>2.02643<span style=""> </span><span style=""> </span>20.2684</b></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">pV<span style=""> </span>-55.9879<span style=""> </span>1393.39<span style="">
</span>1391.81<span style=""> </span>-22.9985<span style=""> </span>-230.031</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">#Surf*SurfTen<span style=""> </span>218.21<span style=""> </span>4871.45<span style="">
</span>4871.37<span style=""> </span>-9.30662<span style=""> </span>-93.0848</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">T-HEX<span style=""> </span>297.366<span style=""> </span>12.086<span style="">
</span>11.4021<span style=""> </span>1.38812<span style=""> </span>13.884</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">Lamb-HEX<span style=""> </span>1.00011 0.000588089
0.000561362 -6.07045e-05 -0.000607166</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">Heat
Capacity Cv:<span style=""> </span>12.5027 J/mol K (factor
= 0.0016519)</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">Isothermal
Compressibility: 0.00011012 /bar</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<span style="font-size: 11pt; font-family: Arial;">Adiabatic
bulk modulus:<span style=""> </span>9080.99<span style=""> </span>bar</span>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"> </span></p>
with mdp file:<br>
> ; Pressure coupling: Pressure coupling is not on<br>
> Pcoupl = berendsen<br>
> tau_p = 0.5<br>
> compressibility = 4.5e-5<br>
> ref_p = 1.0<br><br><br>Thanks,<br><input id="gwProxy" type="hidden"><input onclick="jsCall();" id="jsProxy" type="hidden"><div id="refHTML"></div>