Regards
Vinoth
On Fri, Oct 29, 2010 at 4:42 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
vinothkumar mohanakrishnan wrote:
Hi Justin
Thank you for your comments. Yes i want to concatenate two
systems such that their cross sections are same ( X and Y axis
length are same for both the boxes) allowing only the Z axis to
change. The above procedure was employed in the literature and
latter they combined two boxes.
what i want to know ultimately is can i go ahead with this
pressure ( i have no problem with temperature and density) for
water to create an interface by combining two boxes?
Yes, it's fine. Regardless, you're going to have to do more
equilibration after you've assembled the system.
-Justin
Regards
Vinoth
On Fri, Oct 29, 2010 at 4:21 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
vinothkumar mohanakrishnan wrote:
Hi Mark
How come 7 +/- 500 bar is approximately 1 bar. Can you
explain
it more clearly? It will be of more useful to me to
understand
the concept.
Suppose you do two simulations. In one, the result is
7+/-500 and
in the other, the result is 1+/-500. Even though the latter
achieves the preferred result (average pressure of 1 bar),
statistically, there is no difference between these two results
because of the huge standard deviations in the data.
One more thing, density (from g_energy command) of water is
found to low (expected 1000) after NPT is equilibration. why?
given below is my average density value. Can i proceed
with this
density value?
Energy Average RMSD Fluct.
Drift Tot-Drift
-------------------------------------------------------------------------------
Density (SI) 979.37 14.3238 14.2431
-0.0525784 -5.25789
Real water and SPC water are different. I don't know that
there is
any water model out there that perfectly reproduces all the
properties of water. A density around 980 sounds about right
for SPC.
A comment on your previous approach: you're hoping to achieve the
same box dimensions for two different systems in order to
concatenate them and make an interfacial system? It would be far
easier to create the organic phase, extend the box in z, and then
solvate with genbox.
-Justin
Regards
Vinoth
On Fri, Oct 29, 2010 at 2:06 PM, Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>>> wrote:
On 29/10/2010 6:39 PM, vinothkumar mohanakrishnan wrote:
I am using the semiisotropic pressure scaling
because i
want the
box size to remain the same as that of the
original box
size in X
and Y axis and want to change it only on the Z
axis. I am
doing
this because at a latter stage i want to create an
interface with
organic solvent where i need the cross sections (X
and Y axis
length) of both the box should be the same.
what i should do now get the pressure of 1 bar?
7 +/- 500 *is* approximately 1 bar, and hardly any
better an
approximation than 1 +/- 500. If you want lower
fluctuations,
use a
larger system and run for a much longer time. Or, since
you'll have
to re-equilibrate once you combine the solvent boxes,
don't
bother.
Mark
Has no one has got the pressure of water to be
close to 1
bar in
GROMACS till now?
Regards
Vinoth
On Fri, Oct 29, 2010 at 12:54 PM, David van der Spoel
<sp...@xray.bmc.uu.se
<mailto:sp...@xray.bmc.uu.se> <mailto:sp...@xray.bmc.uu.se
<mailto:sp...@xray.bmc.uu.se>>
<mailto:sp...@xray.bmc.uu.se
<mailto:sp...@xray.bmc.uu.se> <mailto:sp...@xray.bmc.uu.se
<mailto:sp...@xray.bmc.uu.se>>>>
wrote:
On 2010-10-29 09.08, vinothkumar
mohanakrishnan wrote:
Hi Mark
I read the link before posting the
question. even
though
the fluctation
is between 500-600 (as said in the link)
bar the
average
pressure is
around 7.4 bar. my concern is the average
pressure?.
Because at a latter
stage i am going to combine this water box
with
another
organic solvent
and i want to avoid any complications there.
Think again of what you just wrote. Your value
is 7
+/- 500.
In fact according to normal statistical rules you
should round
the value of 7 to 0. If you want more accurate
number you
could increase the box size by a factor of 100.
By the way, why are you using semiisotropic
pressure
scaling
in a water box?
Regards
Vinoth
On Fri, Oct 29, 2010 at 12:22 PM, Mark Abraham
<mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>>>> wrote:
On 29/10/2010 5:48 PM, vinothkumar
mohanakrishnan wrote:
Hi Gromacians
I want to do equilibration of water
(spc
model)
first in the NVT
ensemble and then in the NPT
ensemble to
maintain a
temperature
of 300K and a pressure of 1 bar
respectively. The NVT
equilibration works fine and the
average
temperature turns out
to be 299.229 K.
Energy Average
RMSD Fluct.
Drift Tot-Drift
------------------------------
-------------------------------------------------
Temperature 299.229
10.3092 10.2463
0.0393873 3.93877
Heat Capacity Cv: 12.494 J/mol K
(factor =
0.00118698)
when i do NPT equilibration i am not
getting the
desired
pressure as 1 bar or atleast close
to 1 bar
(between 1-1.4 bar).
In the mdp file i used
semiisotropic pressure
coupling type
because i want to fix the length of the
box same on
two axis as
that of the original box size and
want to
change it
only on one
axis. can any one tell me why iam not
getting the
desired
pressure of 1 bar?.
This looks normal for a smallish water
system over
100ps. See
http://www.gromacs.org/Documentation/Terminology/Pressure
Mark
Energy Average
RMSD Fluct.
Drift Tot-Drift
-------------------------------------------------------------------------------
Pressure (bar) 7.4339
574.052 573.574
0.812129 81.2138
Given below is my mdp file (NPT
equilibration). any
help is
highly appreciated.
title = DCE NVT equilibration
cpp = usr/bin/cpp
integrator = md
nsteps = 100000
dt = 0.001
nstxout = 100
nstvout = 100
nstenergy = 100
nstlog = 100
ns_type = grid
nstlist = 1
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = Cut-off
rvdw = 1.0
pme_order = 4
fourierspacing = 0.16
pbc = xyz
tcoupl = V-rescale
tc-grps = system
tau_t = 0.1
ref_t = 300
pcoupl = berendsen
pcoupltype = semiisotropic
tau_p = 0.5
ref_p = 1.0 1.0
compressibility = 0.0 4.5e-5
DispCorr = Enerpres
gen_vel = yes
gen_temp = 300
gen_seed = 173529
Regards
Vinoth
--
gmx-users mailing list
gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>>>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search
before posting!
Please don't post (un)subscribe requests to
the list.
Use the www
interface or send it to
gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>>>.
Can't post? Read
http://www.gromacs.org/Support/Mailing_Lists
-- David van der Spoel, Ph.D.,
Professor of
Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:
+46184714205.
sp...@xray.bmc.uu.se
<mailto:sp...@xray.bmc.uu.se> <mailto:sp...@xray.bmc.uu.se
<mailto:sp...@xray.bmc.uu.se>>
<mailto:sp...@xray.bmc.uu.se
<mailto:sp...@xray.bmc.uu.se> <mailto:sp...@xray.bmc.uu.se
<mailto:sp...@xray.bmc.uu.se>>>
http://folding.bmc.uu.se
-- gmx-users mailing list
gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search
before
posting!
Please don't post (un)subscribe requests to
the list.
Use the
www interface or send it to
gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>>.
Can't post? Read
http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
Please don't post (un)subscribe requests to the list.
Use the
www interface or send it to
gmx-users-requ...@gromacs.org <mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>>.
Can't post? Read
http://www.gromacs.org/Support/Mailing_Lists
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
-- gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
