Reply inline...<br><br><div class="gmail_quote">On Thu, Jul 15, 2010 at 9:54 AM, 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:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
<br>
Sai Pooja wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Reply inline...<div class="im"><br>
<br>
On Thu, Jul 15, 2010 at 9:41 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Sai Pooja wrote:<br>
<br>
Hi,<br>
<br>
I have a system of 3600 LJ particles in a plane (using<br>
freeze-dimension option in z). I am running npt runs using<br>
Semi-isotropic pressure coupling with Parrinello-Rahman<br>
barostat. I have a few concerns:<br>
<br>
1) On the gromacs website, a webpage mentions that this type of<br>
pressure coupling may not be accurate<br>
<br>
<br>
Please provide a link when making this kind of statement.<br>
<a href="http://www.gromacs.org/index.php?title=Developer_Zone/Programming_Guide/Barostat&highlight=parrinello-rahman" target="_blank">http://www.gromacs.org/index.php?title=Developer_Zone/Programming_Guide/Barostat&highlight=parrinello-rahman</a><br>
<<a href="http://www.gromacs.org/index.php?title=Developer_Zone/Programming_Guide/Barostat&highlight=parrinello-rahman" target="_blank">http://www.gromacs.org/index.php?title=Developer_Zone/Programming_Guide/Barostat&highlight=parrinello-rahman</a>><br>
</div></blockquote>
<br>
Bugzilla entry 14 is ancient, and has long since been resolved:<br>
<br>
<a href="http://www.gromacs.org/About_Gromacs/Release_Notes/Revisions_in_4.0#Resolved_issues" target="_blank">http://www.gromacs.org/About_Gromacs/Release_Notes/Revisions_in_4.0#Resolved_issues</a><div><div></div><div class="h5">
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
2) It takes a really long time for the system to reach the<br>
reference pressure > 500ns. Particularly the Pxx, Pyy terms are<br>
very different and take an extremely long time to converge to a<br>
common value.<br>
<br>
integrator = md<br>
dt = 0.001<br>
nsteps = 50000000<br>
<br>
; OUTPUT CONTROL OPTIONS<br>
nstxout = 0 ; No output, except for last frame<br>
(coordinates)<br>
nstvout = 0 ; No output, except for last frame<br>
(velocities)<br>
nstfout = 0 ; No output, except for last frame<br>
(forces)<br>
nstlog = 1000000 ; Write every nth step to the log<br>
nstenergy = 1000000 ; Write energies at every n step<br>
nstxtcout = 1000000 ; Do not write a compressed tr<br>
<br>
; NEIGHBORSEARCHING PARAMETERS<br>
nstlist = 10<br>
ns-type = Grid<br>
pbc = xyz<br>
rlist = 0.9<br>
<br>
; OPTIONS FOR ELECTROSTATICS AND VDW<br>
coulombtype = Cut-off<br>
rcoulomb = 1.1225<br>
vdw-type = User<br>
rvdw = 1.1225<br>
table-extension = 0<br>
<br>
; Temperature coupling<br>
tcoupl = nose-hoover<br>
tc-grps = ARAR<br>
tau_t = 0.1<br>
ref_t = 120.2717<br>
<br>
; Pressure coupling<br>
pcoupl = Parrinello-Rahman<br>
pcoupltype = semiisotropic<br>
tau-p = 1.0 1.0<br>
compressibility = 1e-5 0 ;Dont know<br>
ref-p = 69 0<br>
<br>
<br>
;Generate velocities for startup run<br>
gen_vel =no<br>
gen_temp =120.2717<br>
gen_seed =-1<br>
<br>
;Non equilibrium MD steps<br>
freezegrps =ARAR<br>
freezedim =N N Y <br>
;Constraints<br>
constraints = all-bonds<br>
constraint_algorithm = Lincs<br>
lincs_order = 4<br>
lincs_iter = 1<br>
lincs_warnangle = 90 ;unconstrained_start = no<br>
;shake_tol = 0.0001<br>
<br>
</blockquote>
<br></div></div>
Do you run any equilibration prior to applying these parameters? Both N-H and P-R allow for wide fluctuations in temperature and pressure, respectively, which are exacerbated by systems that are not sufficiently equilibrated. Hence it could take a very long time if you do not equilibrate well using, i.e. a weak coupling scheme first.<br>
<br></blockquote><div><br></div><div>I usually start with a pressure nearby. For example, I start with a system which was equilibrated at p=71 and then run npt at p=69. Is that not sufficient?</div><div><br></div><div>Pooja</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
<br>
<br>
<br>
What was your equilibration protocol? What are your .mdp settings?<br>
<br>
-Justin<br>
<br>
<br>
Pooja<br>
<br>
-- Quaerendo Invenietis-Seek and you shall discover.<br>
<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></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><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>
-- 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 <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
posting!<br>
Please don't post (un)subscribe requests to the list. Use the www<br>
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/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
<br>
<br>
<br>
-- <br>
Quaerendo Invenietis-Seek and you shall discover.<br>
</div></blockquote><div><div></div><div class="h5">
<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>
-- <br>
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/search" target="_blank">http://www.gromacs.org/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/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Quaerendo Invenietis-Seek and you shall discover.<br>