On 2011-03-12 07.52, Thomas Koller wrote:
Thanks,
the equation for the heat capacity is:
c(P) = delta(H(average))/delta(T(average))
So do it have to take the fluctuations (which are listed with g_energy) of
U(tot) and pV as well as of T to calculate c(P)? The problem is the delta.
The same i
On 2011-03-12 06.09, Denny Frost wrote:
I am running MD simulations on Liquid/Liquid interfaces and measuring
the interfacial tension between them. I have found that the readings in
NVT simulations are close to experimental values, but have a lot of
variation. I run NPT simulations on the exact
On 2011-03-12 08.54, mohsen ramezanpour wrote:
Dear All
How can I read and work on outputs of one version of Gromacs with tools
of other version?
Because I have run my program on cluster(version 4.5.3) ,but I need to
work with them in v.4.0.7
Suppose I have to work with this version and there
Hi mohsen,
I think that "I need to work with them in v.4.0.7" means that you need
to ANALYZE your trajectory with gmx4.0.7. Is it correct?
If this is the case, problem should not arise with trajectory files.
You should have problems only with topology that is not back-compatible.
However, for
thanks for your replies.
Yes,you are correct.
Actually I need to analyze my trajectories and energy files .
I tried but I couldn't use from my energy.edr file in old version(4.0.7),it
say:
"it seems you want to read edr file from version 4.1 or latter with old
version "
Please let me know how can
The exact Error is this:
Program g_energy, VERSION 4.0.7
Source code file: ../../../../src/gmxlib/enxio.c, line: 118
Fatal error:
You are trying to read an edr file of GROMACS version 4.1 or later with
GROMACS version 4.0
On Sat, Mar 12, 2011 at 2:46 PM, mohsen ramezanpour <
ramezanpour.moh.
Hello,
I am using g_covar vailable in user contributed section (by Ran Friedman)
the description available for the package is as follows:
"This package contains a modified version of g_covar, which can print a
matrix
of atomic correlation coefficients (with -xpmc) and write all pairs with a
correl
On 2011-03-12 12.23, mohsen ramezanpour wrote:
The exact Error is this:
Program g_energy, VERSION 4.0.7
Source code file: ../../../../src/gmxlib/enxio.c, line: 118
Fatal error:
You are trying to read an edr file of GROMACS version 4.1 or later with
GROMACS version 4.0
Upgrade gromacs.
On
Hi,
I'm about to simulate a disaccaride in water.
Reading through the paper from Hansen and Hünenberger:
A reoptimized GROMOS force field for hexopyranose-based carbohydrates
accounting for the relative free energies of ring conformers, anomers,
epimers, hydroxymethyl rotamers, and glycosidic
英雄不再寂寞 wrote:
Dear gmxers,
I want to perform a constant-NPT MD simulation using gmx. By default,
a,b,c of 3D pbc box can change to compatile with the density. Whether
can gmx change a,b of 3D pbc box but unchange c? Please give me some
hints. Thanks a lot.
Set the compressibility of w
Hi All,
I believe I have a resolution to all of this. It comes down to compilers and
FFTW. I had always used the same compilers to build all my Gromacs versions
(gcc-4.2.2 on Linux, gcc-3.3 on OSX) with the same version of FFTW (3.0.1),
primarily for reasons of continuity. Bug 715 that I p
Hi,
As stated below the upper half of the triangle shows correlations having r>0.5
or r<-0.5, that is |r|>0.5
Ran
From: bipin singh [bipinel...@gmail.com]
Sent: 12 March 2011 12:27
To: Discussion list for GROMACS users
Cc: r.fried...@bioc.uzh.ch
Subject: R
I dont know exactly what you mean. Here you can see my output data:
Energy AverageRMSDFluct. Drift Tot-Drift
---
Potential -48.8499 1.82144 1.81841 -0.00781553 -0.3638
Kin
David,
I have a question that is still related to your reply. If the bulk
liquid NPT and the interfacial liquid-vapor NVT simulations are
performed using dispersion corrections to the pressure and energy,
while the intefacial liquid-liquid NPAT simulation don't use any
correction, can we say that
That are different way:
1. Performing analysis directly on the cluster where 4.5.3 is installed
2. Installing gmx 4.5.3 on you laptop.
3. Writing a program that converts from 4.5.3 to 4.0.7
Il 12/03/2011 12:16, mohsen ramezanpour ha scritto:
thanks for your replies.
Yes,you are correct.
Actua
On 2011-03-12 14.00, Thomas Koller wrote:
I dont know exactly what you mean. Here you can see my output data:
Energy AverageRMSDFluct. Drift Tot-Drift
---
Potential -48.849
I have run NPT simulations using isotropic and semiisotropic coupling with
the same results. I have never done coupling in just one direction though,
how do you do this?. I have never used Dispersion corrections. It seems to
me that this would help, rather than hurt though since, as Aldi said, i
Dear Gromacs Users,
I'm using "trjorder" with the following options:
$ trjorder -f systemWithSolv.xtc -n system.atom.ndx -s system.pdb -r
0.35 -nshell system0.35.nshell.xvg
As the first group I select all the atoms of a single TYR residue,
which is part of a larger protein. As the second group
On 2011-03-12 16.45, Denny Frost wrote:
I have run NPT simulations using isotropic and semiisotropic coupling
with the same results. I have never done coupling in just one direction
though, how do you do this?. I have never used Dispersion corrections.
It seems to me that this would help, rathe
Is that using anisotropic pressure coupling?
On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel
wrote:
> On 2011-03-12 16.45, Denny Frost wrote:
>
>> I have run NPT simulations using isotropic and semiisotropic coupling
>> with the same results. I have never done coupling in just one direction
Henri Mone wrote:
Dear Gromacs Users,
I'm using "trjorder" with the following options:
$ trjorder -f systemWithSolv.xtc -n system.atom.ndx -s system.pdb -r
0.35 -nshell system0.35.nshell.xvg
As the first group I select all the atoms of a single TYR residue,
which is part of a larger protein
On 2011-03-12 16.59, Denny Frost wrote:
Is that using anisotropic pressure coupling?
yes.
just try it
On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel
mailto:sp...@xray.bmc.uu.se>> wrote:
On 2011-03-12 16.45, Denny Frost wrote:
I have run NPT simulations using isotropic and
Thanks for answering that question about dispersion, that makes sense.
Also, The values I currently get with NPT are around 58 mN/m, while the
average values I get for NVT are around 16 mN/m, but with a variance of
nearly 100% of that value. I'm beginning to see why you only do pressure
coupling i
On 2011-03-12 17.17, Denny Frost wrote:
Thanks for answering that question about dispersion, that makes sense.
Also, The values I currently get with NPT are around 58 mN/m, while the
average values I get for NVT are around 16 mN/m, but with a variance of
nearly 100% of that value. I'm beginning
No, it requires six, acutally, for aniisotropic coupling. I decided to use
semi-isotropic coupling with the xy compressibilities set to 4.5e-15 (it
won't accept 0). This should keep the walls parallel to the z axis from
moving and accomplish the same thing. Does this sound right?
On Sat, Mar 12
On 2011-03-12 17.28, Denny Frost wrote:
No, it requires six, acutally, for aniisotropic coupling. I decided to
use semi-isotropic coupling with the xy compressibilities set to 4.5e-15
(it won't accept 0). This should keep the walls parallel to the z axis
from moving and accomplish the same thin
It won't take zero with the berendsen thermostat, but I only wish to do weak
coupling for now. Yes, I only specified the two values for semiisotropic.
What I'm asking is will this setup only do z-pressure coupling?
On Sat, Mar 12, 2011 at 9:32 AM, David van der Spoel
wrote:
> On 2011-03-12 17.28
On 2011-03-12 17.36, Denny Frost wrote:
It won't take zero with the berendsen thermostat, but I only wish to do
weak coupling for now. Yes, I only specified the two values for
semiisotropic. What I'm asking is will this setup only do z-pressure
coupling?
http://manual.gromacs.org/current/onli
Based on a preliminary test using multiple threads, the issue is not
resolved.
This leads me to believe that my Unit Cell is not built properly.
Below is the procedure used to build the unit cell. I have reviewed it many
times, but I would appreciate any input regarding potential improvements,
sp
Steve Vivian wrote:
Based on a preliminary test using multiple threads, the issue is not
resolved.
This leads me to believe that my Unit Cell is not built properly.
Below is the procedure used to build the unit cell. I have reviewed it many
times, but I would appreciate any input regarding po
Steve Vivian wrote:
Based on a preliminary test using multiple threads, the issue is not
resolved.
This leads me to believe that my Unit Cell is not built properly.
Below is the procedure used to build the unit cell. I have reviewed it many
times, but I would appreciate any input regarding po
On 03/12/2011 12:51 PM, Justin A. Lemkul wrote:
Getting hard to follow, so I put my new comments in blue.
Output from Energy Minimization
Steepest Descents converged to Fmax < 1000 in 1814 steps
Potential Energy = -3.81270276926664e+05
Maximum force = 9.38712770623942e+02 on atom 2292
Norm
Steve Vivian wrote:
On 03/12/2011 12:51 PM, Justin A. Lemkul wrote:
Getting hard to follow, so I put my new comments in blue.
Output from Energy Minimization
Steepest Descents converged to Fmax < 1000 in 1814 steps
Potential Energy = -3.81270276926664e+05
Maximum force = 9.387127706239
Steve Vivian wrote:
On 03/12/2011 01:36 PM, Justin A. Lemkul wrote:
Steve Vivian wrote:
On 03/12/2011 12:51 PM, Justin A. Lemkul wrote:
Getting hard to follow, so I put my new comments in blue.
Output from Energy Minimization
Steepest Descents converged to Fmax < 1000 in 1814 steps
Poten
Dear All
I run a simulation for 4 days.
Unfortunately it terminated,but not completely,1 steps from 2 has
done.
Is there any way to run the continue of my files?
Thanks in advance for your guidances
Best Regards
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/
On 03/12/2011 02:10 PM, Justin A. Lemkul wrote:
Steve Vivian wrote:
On 03/12/2011 01:36 PM, Justin A. Lemkul wrote:
Steve Vivian wrote:
On 03/12/2011 12:51 PM, Justin A. Lemkul wrote:
Getting hard to follow, so I put my new comments in blue.
Output from Energy Minimization
Steepest Desc
Hi All,
Unfortunately, my positive news was a false alarm. Intermediate values of
lambda are sporadically failing at different times. Some jobs exit at time
zero, others last somewhat longer (several hundred ps) before failing. I'm
going to keep working on the suggestions I got before abou
-cpi state.cpt -append
try to add those two options at the end of your mdrun
lina
On Sun, Mar 13, 2011 at 5:53 AM, mohsen ramezanpour <
ramezanpour.moh...@gmail.com> wrote:
> Dear All
>
> I run a simulation for 4 days.
> Unfortunately it terminated,but not completely,1 steps from 2 h
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