Hi Dallas / all<br><br>I looked up at the pressure coupling section and i found how to keep the box size same for two axis and change only one axis (i used semiisotropic pressure coupling type) but when i did that the average pressure i get after the run is negative where as i want it be close to 1 bar?. i dont know what might have gone wrong.<br>
<br>Energy Average RMSD Fluct. Drift Tot-Drift<br>-------------------------------------------------------------------------------<br>Pressure (bar) -661.673 675.593 674.292 -0.725677 -145.136<br>
<br>similary when i give g_energy -f npt.edr -o density.xvg the density option is not there to select it interactively. hence i am not able to plot the density graph.why?<br><br>1 Bond 2 Angle 3 Ryckaert-Bell. 4 LJ-14 <br>
5 Coulomb-14 6 LJ-(SR) 7 Disper.-corr. 8 Coulomb-(SR) <br>9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy <br>13 Conserved-En. 14 Temperature 15 Pressure-(bar) 16 Vir-XX <br>
17 Vir-XY 18 Vir-XZ 19 Vir-YX 20 Vir-YY <br>21 Vir-YZ 22 Vir-ZX 23 Vir-ZY 24 Vir-ZZ <br>25 Pres-XX-(bar) 26 Pres-XY-(bar) 27 Pres-XZ-(bar) 28 Pres-YX-(bar) <br>
29 Pres-YY-(bar) 30 Pres-YZ-(bar) 31 Pres-ZX-(bar) 32 Pres-ZY-(bar) <br>33 Pres-ZZ-(bar) 34 #Surf*SurfTen 35 Mu-X 36 Mu-Y <br>37 Mu-Z 38 T-System 39 Lamb-System <br>
<br> and i have given my mdp file below. any help is highly appreciated.<br><br>title = DCE NPT equilibration <br>integrator = md <br>nsteps = 200000<br>dt = 0.001 <br>nstxout = 1000 <br>
nstvout = 1000 <br>nstenergy = 1000 <br>nstlog = 1000 <br>constraint_algorithm = lincs <br>constraints = all-bonds <br>lincs_iter = 1 <br>lincs_order = 4 <br>ns_type = grid <br>
nstlist = 5 <br>rlist = 1.0 <br>rcoulomb = 1.0 <br>rvdw = 1.0 <br>coulombtype = PME <br>pme_order = 4 <br>fourierspacing = 0.16 <br>tcoupl = V-rescale <br>
tc-grps = system <br>tau_t = 0.1 <br>ref_t = 300 <br>pcoupl = Parrinello-Rahman <br>pcoupltype = semiisotropic <br>tau_p = 2.0 2.0 <br>ref_p = 1.0 1.0 <br>
compressibility = 0.0 4.5e-5 <br>pbc = xyz <br>DispCorr = EnerPres <br>gen_vel = no <br><br>Regards<br>Vinoth<br><br><br><div class="gmail_quote">On Tue, Oct 26, 2010 at 5:33 AM, Dallas Warren <span dir="ltr"><<a href="mailto:Dallas.Warren@monash.edu">Dallas.Warren@monash.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div link="blue" vlink="purple" lang="EN-US">
<div><div class="im">
<p class="MsoNormal">>I performed md simulation of 108 dichloroethane
molecules in isothermal-isobaric ensemble with the box size</p>
<p class="MsoNormal">>3.002*2.17*2.17. after the simulation my box size has
changed considerably from the initial size to 2.87882 2.08095</p>
<p class="MsoNormal">>2.08095.why this happens?</p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
</div><p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Density was obviously too lower under the conditions of the
simulation. Look at the change of pressure, volume and density for the box
during that simulation.</span></p><div class="im">
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal">>my second question is can i have a control over the box
dimensions changes during md (i.e when the box dimensions</p>
<p class="MsoNormal">>changes during md i want to change it only on one
axis(say x axis) and want to keep the length of the other two axis (say</p>
<p class="MsoNormal">>y and z) same as that of my initial box size? any help
is highly apprecited.</p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
</div><p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Look at the pressure coupling settings, look at anisotropic
pressure coupling.</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; color: rgb(31, 73, 125);">Catch ya,<br>
<br>
Dr. Dallas Warren</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; color: rgb(31, 73, 125);">Medicinal Chemistry and Drug Action</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; color: rgb(31, 73, 125);">Monash Institute of Pharmaceutical Sciences</span><span style="font-size: 10pt; color: rgb(31, 73, 125);">,
Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<a href="mailto:dallas.warren@monash.edu" target="_blank">dallas.warren@monash.edu</a></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; color: rgb(31, 73, 125);">+61 3 9903 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a
nail.</span><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
</div>
</div>
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