Hello,<br><br>Thank you. I am looking at potential energies to calculate vaporization heat. I wanted to know how the fact that berendsen does not lead to correct ensemble is affecting total potential energy of the system. I have an unclear image of "correct ensemble". Does this mean whatever output I am getting from my runs are unreliable? <br>
<br>Appreciate any clarification. <br><br>Thank you,<br>Best,<br><br><div class="gmail_quote">On 15 August 2011 19:34, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</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 bgcolor="#FFFFFF" text="#000000"><div class="im">
On 16/08/2011 7:05 AM, Elisabeth wrote:
<blockquote type="cite">Dear all,<br>
<br>
I noticed that applying Parrinello-Rahman (PR) pressure coupling
even after equilibration with berendsen does not lead to target
value for pressure when <br>
<br>
; Bonds<br>
constraints = none<br>
<br>
is used.</blockquote>
<br></div>
The use of constraints and the integration step size is linked.
Roughly speaking, no constraints should accompany a 0.5 fs time
step, H-bond constraints with 1fs and all constraints with 2fs.
Haphazard changes to .mdp files have all kinds of these "gotchas".<div class="im"><br>
<br>
<blockquote type="cite"> I tried Berendsen for to get fixed pressure ( 50 bar)
but in the next run PR even for long time is giving 52 bar. This
is the case for other target pressures too.<br>
</blockquote>
<br></div>
You need to be sure to collect statistics only after equilibration,
and consider whether the observed variation is consistent with
convergence to a given value.<div class="im"><br>
<br>
<blockquote type="cite"><br>
So this made me select Berenden which is giving target pressure
values but my concern is whether my results are reliable because
BR does not give the exact ensemble as PR. I read somewhere on the
list that fluctuation properties can not be calculated when BR is
used. What does "fluctuation property" mean?<br>
</blockquote>
<br></div>
BR does not produce the correct ensemble. I forget the details about
why, but there are references in the T-coupling section of the
manual you should consider.<div class="im"><br>
<br>
<blockquote type="cite">Does this mean that any property calculated form
fluctuations of some other quantity can not be obtained>? like
heat capacity which is defined based on enthalpy fluctuations? <br>
</blockquote>
<br></div>
IIRC, yes.<div class="im"><br>
<br>
<blockquote type="cite">I am interested in potential energy terms (g_energy
bonded/non boned terms) </blockquote>
<br></div>
I routinely struggle to see why people think they can learn anything
from these.<div><div></div><div class="h5"><br>
<br>
<blockquote type="cite">and structural properties like rdf for a number of
polymer molecules, system size around 3000 atoms. <br>
<br>
Thank you for your comments.<br>
Best,<br>
<br>
constraints = none <br>
<br>
; Run control <br>
integrator = md <br>
dt = 0.001 <br>
nsteps = 5000000 <br>
nstcomm = 100 <br>
<br>
<br>
nstenergy = 100 <br>
nstxout = 100 <br>
nstlist = 10 <br>
ns_type = grid <br>
<br>
coulombtype = Shift <br>
vdw-type = Shift <br>
rcoulomb-switch = 0 <br>
rvdw-switch = 0.9 ;0 <br>
<br>
; Cut-offs<br>
rlist = 1.25 <br>
rcoulomb = 1.0 <br>
rvdw = 1.0 <br>
<br>
Tcoupl = v-rescale <br>
tc-grps = System <br>
tau_t = 0.1 <br>
ref_t = 300 <br>
<br>
Pcoupl = berendsen <br>
Pcoupltype = isotropic <br>
tau_p = 1 <br>
compressibility = 3.5e-5 <br>
ref_p = 10 <br>
<br>
<br>
gen_vel = no<br>
gen_temp = 300.0 <br>
gen_seed = 173529 <br>
<br>
<br>
<br>
<br>
<br>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div></div></div>
<br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">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<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">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></blockquote></div><br>