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>> 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>>> 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
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