Hello, <br><br>I followed the hints. I did several NPT runs and I found out pressure above 100 eg 120 bar gives final boxsize close to volume of box I want. But I dont know why pressure given by g_energy is totally different. <br>
<br>1- I looked at values in xvg file and I notoced pressre starts froma very low value, also takes negative and postive values. If I am doing NPT why P is changing ?<br>2- at the end of xvg file I see final dimensions are 2*2*2 . Also I checked the size in ngmx and I see that long chain is compressing very nicely and takes a very convoluted conformation in a very small size. I selected 1000 ps but after 727 ps simulation stops (it seems box size can not be reduced further).However, When I open the gro file PE60_after_MD dimensions are 22*22*22! :( why is this happening?<br>
<br><br>Energy Average RMSD Fluct. Drift Tot-Drift<br>-------------------------------------------------------------------------------<br>Angle 725.016 41.3878 36.4581 0.0790551 67.8611<br>
Ryckaert-Bell. 231.804 29.096 25.866 0.0537685 46.155<br>LJ-14 161.418 8.09535 7.98175 0.00545371 4.68147<br>Coulomb-14 -87.8111 8.74814 7.24162 0.0198065 17.0019<br>
LJ (SR) -145.619 82.9315 38.527 -0.296365 -254.401<br>Coulomb (SR) 190.015 14.0939 11.1829 -0.0346165 -29.7149<br>Potential 1074.82 73.9367 60.258 -0.172898 -148.416<br>
Kinetic En. 899.733 29.9816 29.9813 0.000554359 0.475863<br>Total Energy 1974.56 67.628 52.4374 -0.172344 -147.94<br>Temperature 299.757 9.98875 9.98864 0.000184692 0.15854<br>
<b>Pressure (bar) -1.43379 141.354 141.205 -0.0261305 -22.4305</b><br>Cons. rmsd () 5.12607e-06 4.18181e-07 3.98738e-07 5.08597e-10 4.3658e-07<br>Box-X 10.7454 7.6259 2.33711 -0.0292936 -25.1457<br>
Box-Y 10.7454 7.6259 2.33711 -0.0292936 -25.1457<br>Box-Z 10.7454 7.6259 2.33711 -0.0292936 -25.1457<br>Density (SI) 32.6368 57.0897 38.1186 0.171508 147.222<br>
pV -5.00443 428.488 428.332 -0.0466916 -40.0802<br>Vir-XX 321.928 424.592 424.396 0.051996 44.6335<br>Mu-X 0.00138297 0.33292 0.332911 -9.74152e-06 -0.00836214<br>
Lamb-System 1.00002 0.000363012 0.000363011 -3.17825e-09 -2.72822e-06<br>Heat Capacity Cv: 12.4926 J/mol K (factor = 0.00111041)<br><br>3- The systems seems not to be equilibrated yet. eg LJ SR remains constant for a while and goes down and its not reaching a plateau after 720 ps (where simulation stops). <br>
<br>4- When I choose p 200bar , compression continues till 420 ps. Actually chain takes a specific conformation in such a way that it can not get compressed further and simulation stops even before former trial (p 120 bar).<br>
a simple question:<br>5- About tc groups in mdpfile: actually I see people having names like protein SOL as their groups but I am wondering how I can set the name "polymer". I thought this comes form the [system] or [molecule] in top file but its not so (or thought may names are coming form index file). If I want to add hexane to PE and calculate energies I need to have these two groups separately. for PE I have three residues Eth EthB EthE.Could you please tell me how can I include them in one single group 'Polymer"? and use this name in mdp file?<br>
<br>Thanks for your help.<br><br>