Hi Justin <br><br>Thank you very much for your comments. I actually found that after posting the question. sorry I have a new question i did NPT equilibration of DCE molecules and the average pressure turns out to be 3.4726 (bar) where as i want the pressure it to be 1 bar. what further i need to do?.below is what i got from the g_energy command.<br>
<br>Energy Average RMSD Fluct. Drift Tot-Drift<br>-------------------------------------------------------------------------------<br>Pressure (bar) 3.47263 767.297 765.878 0.8078 161.561<br>
<br> below is my mdp file any help is highly appreciated<br><br>title = DCE NVT equilibration <br>cpp = usr/bin/cpp<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 = shake <br>constraints = none <br>unconstrained_start = yes <br>shake_tol = 0.0001 <br>
morse = no <br>ns_type = grid <br>nstlist = 5 <br>rlist = 1.0 <br>coulombtype = PME <br>rcoulomb = 1.0 <br>vdwtype = Cut-off <br>rvdw = 1.0 <br>
pme_order = 4 <br>fourierspacing = 0.16 <br>pbc = xyz <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>DispCorr = Enerpres <br>gen_vel = yes <br>gen_temp = 300 <br>
gen_seed = 173529<br><br>Regards<br>Vinoth<br><br><br><br><div class="gmail_quote">On Tue, Oct 26, 2010 at 4:34 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.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 class="im"><br>
<br>
vinothkumar mohanakrishnan wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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>
</blockquote>
<br></div>
All of the above suggests you've gotten your files confused and you're analyzing an .edr file from an NVT run, not NPT. If indeed you did NPT, the density term would appear below, along with "Volume." The only time when these terms are not written is if the volume of the unit cell is static (i.e., NVT).<div class="im">
<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
1 Bond 2 Angle 3 Ryckaert-Bell. 4 LJ-14 5 Coulomb-14 6 LJ-(SR) 7 Disper.-corr. 8 Coulomb-(SR) 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 13 Conserved-En. 14 Temperature 15 Pressure-(bar) 16 Vir-XX 17 Vir-XY 18 Vir-XZ 19 Vir-YX 20 Vir-YY 21 Vir-YZ 22 Vir-ZX 23 Vir-ZY 24 Vir-ZZ 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 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 nsteps = 200000<br>
dt = 0.001 nstxout = 1000 nstvout = 1000 nstenergy = 1000 nstlog = 1000 constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ns_type = grid nstlist = 5 rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 coulombtype = PME pme_order = 4 fourierspacing = 0.16 tcoupl = V-rescale tc-grps = system tau_t = 0.1 ref_t = 300 pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 2.0 2.0 ref_p = 1.0 1.0 compressibility = 0.0 4.5e-5<br>
</blockquote>
<br></div>
For what its worth, if this is your initial equilibration, using Parrinello-Rahman coupling may not be your best choice. If your system is far from equilibrated, the P-R method (in my experience) can allow for wide oscillations, and ultimately system instability. Nothing wrong with Berendsen for your initial equilibration.<br>
<br>
But again, if pressure coupling was actually used, you'd have Volume and Density terms in the .edr file, along with a more sensible value of pressure.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
pbc = xyz DispCorr = EnerPres gen_vel = no <br>
Regards<br>
Vinoth<br>
<br>
<br></div><div class="im">
On Tue, Oct 26, 2010 at 5:33 AM, Dallas Warren <<a href="mailto:Dallas.Warren@monash.edu" target="_blank">Dallas.Warren@monash.edu</a> <mailto:<a href="mailto:Dallas.Warren@monash.edu" target="_blank">Dallas.Warren@monash.edu</a>>> wrote:<br>
<br>
>I performed md simulation of 108 dichloroethane molecules in<br>
isothermal-isobaric ensemble with the box size<br>
<br>
>3.002*2.17*2.17. after the simulation my box size has changed<br>
considerably from the initial size to 2.87882 2.08095<br>
<br>
>2.08095.why this happens?<br>
<br>
<br>
Density was obviously too lower under the conditions of the<br>
simulation. Look at the change of pressure, volume and density for<br>
the box during that simulation.<br>
<br>
<br>
>my second question is can i have a control over the box dimensions<br>
changes during md (i.e when the box dimensions<br>
<br>
>changes during md i want to change it only on one axis(say x<br>
axis) and want to keep the length of the other two axis (say<br>
<br>
>y and z) same as that of my initial box size? any help is highly<br>
apprecited.<br>
<br>
<br>
Look at the pressure coupling settings, look at anisotropic pressure<br>
coupling.<br>
<br>
<br>
Catch ya,<br>
<br>
Dr. Dallas Warren<br>
<br>
Medicinal Chemistry and Drug Action<br>
<br>
Monash Institute of Pharmaceutical Sciences, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br></div>
<a href="mailto:dallas.warren@monash.edu" target="_blank">dallas.warren@monash.edu</a> <mailto:<a href="mailto:dallas.warren@monash.edu" target="_blank">dallas.warren@monash.edu</a>><div class="im"><br>
<br>
+61 3 9903 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to<br>
resemble a nail.<br>
<br>
<br>
<br>
<br>
--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="im"><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at<br>
<a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<div class="im"><br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
<br>
</div></blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br><font color="#888888">
-- <br></font><div><div></div><div class="h5">
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br>