Dear Gromacs users,
I am doing a simulation on CO2/water interface. Two separate simulations (NPT) have been done sucessfully for pure CO2 and pure water systems. Then two CO2 gro files and one water gro files were connected into one single gro files for CO2/water interface
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
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:
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
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
Hello gmx-users,
I am running an NPT simulation with 100 molecules of n-alkane and trying to
impose uni-axial pressure of these molecules using semiisotropic option in
grompp.mdp.
However, as the box seems to distort significantly due to the imposed
pressure which leads to the following error
Yongchul Chung wrote:
Hello gmx-users,
I am running an NPT simulation with 100 molecules of n-alkane and trying
to impose uni-axial pressure of these molecules using semiisotropic
option in grompp.mdp.
However, as the box seems to distort significantly due to the imposed
pressure which leads
On Sun, Oct 25, 2009 at 6:28 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
Yongchul Chung wrote:
Hello gmx-users,
I am running an NPT simulation with 100 molecules of n-alkane and trying
to impose uni-axial pressure of these molecules using semiisotropic option
in grompp.mdp.
However, as
On Sun, Oct 25, 2009 at 6:38 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Yongchul Chung wrote:
Hello gmx-users,
I am running an NPT simulation with 100 molecules of n-alkane and trying
to impose uni-axial pressure of these molecules using semiisotropic option
in grompp.mdp.
However, as
Yongchul Chung wrote:
Also note that haphazardly changing the vdwtype or rvdw can have
negative impacts on your simulation, depending on your chosen force
field's sensitivity to these parameters.
Thank you for pointing this out. I am relatively new to this method so
am taking
Dear All,
I have two basic questions regarding membrane protein simulation. First
regarding Semiisotropic pressure coupling (NPAT) and second regarding comm_grpp
(VCM).
1) If I want to use NPAT ensemble (x/y dimensions of bilayer to be fixed) then
is following the correct way to define?
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