On 2010-07-15 00.44, Anne Kelley wrote:
I am trying to use GROMACS to calculate the phonons (normal modes) of a bulk
crystal, CdSe. I have found a simple force field, Coulomb + Lennard-Jones, in
the literature (Rabani, J. Chem. Phys. 116, 258, 2002) which the author showed
reproduced the
Which among DSSP and g_sas is better for calculating solvent accessible
surface area of proteins?
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Bhanu Prakash.
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Dear All
I used the following command sequentially to prepare file for energy
minimization and subsequent MD run.
1. pdb2gmx -f *.pdb -o seq.gro -p seq.top
2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic
3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top
4. grompp -c
Bhanu Prakash Sandaka wrote:
Using DSSP we can also calcuate the surface area, though it doesn't allow
changes in probe diameter etc. it does calculate the surface area. I just
wish to know whether the performance of DSSP is comparable to g_sas?
Should it be used?
From do_dssp -h:
Note that
shahid nayeem wrote:
Dear All
I used the following command sequentially to prepare file for energy
minimization and subsequent MD run.
1. pdb2gmx -f *.pdb -o seq.gro -p seq.top
2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic
3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro
Hi Justin
These errors are from bond between MET/HIS residue and Heme group of
my protein. I checked for all these nine errors of bond and angle in
th file ffG43a1bon.itp and I couldnt find these defined in this file.
Using other options of force field also gives error at some point.
waiting for
Dear all,
I experienced the same skipping of frames when concatenating several
trajectories together using trjcat as reported in a thread from 2008
(see below). Apparently the problem has not been resolved. I am using
Gromacs 4.0.7 and each original trajectory was about 200ns long with
frames
shahid nayeem wrote:
Hi Justin
These errors are from bond between MET/HIS residue and Heme group of
my protein. I checked for all these nine errors of bond and angle in
th file ffG43a1bon.itp and I couldnt find these defined in this file.
Using other options of force field also gives error
Hi all,
We want to calculate strain-stress relationships with gromacs. Can
anybody please provide some links about how it can be done in terms of
gromacs utilities and keywords?
What is the efficient way to apply strain to the system (expand it)?
Thank you.
Vitaly
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Hi,
I have a system of 3600 LJ particles in a plane (using freeze-dimension
option in z). I am running npt runs using Semi-isotropic pressure coupling
with Parrinello-Rahman barostat. I have a few concerns:
1) On the gromacs website, a webpage mentions that this type of pressure
coupling may not
Sai Pooja wrote:
Hi,
I have a system of 3600 LJ particles in a plane (using freeze-dimension
option in z). I am running npt runs using Semi-isotropic pressure
coupling with Parrinello-Rahman barostat. I have a few concerns:
1) On the gromacs website, a webpage mentions that this type of
Reply inline...
On Thu, Jul 15, 2010 at 9:41 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Sai Pooja wrote:
Hi,
I have a system of 3600 LJ particles in a plane (using freeze-dimension
option in z). I am running npt runs using Semi-isotropic pressure coupling
with Parrinello-Rahman
Sai Pooja wrote:
Reply inline...
On Thu, Jul 15, 2010 at 9:41 AM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Sai Pooja wrote:
Hi,
I have a system of 3600 LJ particles in a plane (using
freeze-dimension option in z). I am running npt runs
Hi,
I am aware there have been many threads on this topic and I have looked at
some of them. I would still like to make this query. I am running an npt
equilibration run for a solvated protein using Charmm27-Tip3p (nocmap). I
ran the simulation for 1ns. The average values of pressure converge to
Reply inline...
On Thu, Jul 15, 2010 at 9:54 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Sai Pooja wrote:
Reply inline...
On Thu, Jul 15, 2010 at 9:41 AM, Justin A. Lemkul jalem...@vt.edumailto:
jalem...@vt.edu wrote:
Sai Pooja wrote:
Hi,
I have a system of 3600
Sai Pooja wrote:
Hi,
I am aware there have been many threads on this topic and I have looked
at some of them. I would still like to make this query. I am running an
npt equilibration run for a solvated protein using Charmm27-Tip3p
(nocmap). I ran the simulation for 1ns. The average values
Sai Pooja wrote:
snip
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
On 2010-07-15 16.01, Justin A. Lemkul wrote:
Sai Pooja wrote:
Hi,
I am aware there have been many threads on this topic and I have
looked at some of them. I would still like to make this query. I am
running an npt equilibration run for a solvated protein using
Charmm27-Tip3p (nocmap). I ran
1. Pressure
For my initial configuration, I run a long nvt run. This gives me a
pressure. Then I run an npt simulation at this prerssure.
The idea is to do expansion runs(decrease pressure so that the system
expands) to get a P vs density curve.
For example, after I determine the pressure of the
Sai Pooja wrote:
1. Pressure
For my initial configuration, I run a long nvt run. This gives me a
pressure. Then I run an npt simulation at this prerssure.
The idea is to do expansion runs(decrease pressure so that the system
expands) to get a P vs density curve.
For example, after I
Its basically a melting process and there is ample of published data on this
(not related to gromacs though). The only reason for using freeze-dimensions
was to avoid using pbc=xy in combination with walls since I thought the
extra interactions due to the walls might make the simulations
Hi All,
I was wondering if there is a way to run simulations in the NPH ensemble in
Gromacs. Does any one have experience doing this?
Thank you
Sapna
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Hi,
You can run a simulation with a barostat but with no temperature
coupling. It's probably a good idea to make sure that the system is
equilibrated in terms of the temperature first (with NPT). Also, I'd use
a small timestep and double precision. Search the literature for
protocols from
Hi,
NOTE 4 [file /fs/home/sm868/llamapooja/ffsb/Setup/nvt.mdp]:
The sum of the two largest charge group radii (0.510406) is larger than
rlist (2.00) - rvdw (2.00)
NOTE 5 [file /fs/home/sm868/llamapooja/ffsb/Setup/nvt.mdp]:
The sum of the two largest charge group radii (0.510406)
I am quite sure that I have properly converted sigma and epsilon from the
Angstroms and Kelvin given in the paper to nm and kJ/mol. I experimented with
changing ewald_rtol from 1e-5 to 1 e-7 while reducing fourierspacing from 0.12
to 0.077, but the effects were negligibly small. The Rabani
hi,all
I'm doing a simulation about the vdw interaction of Graphite and
Carbon Nanotube.
In my model is a trilayer graphite and a CNT which is perpendicular to
the graphite plane,like
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