Hi,
I wanted to numerically determine the gaussian curvature of a phase obtained
by self-assembly of surfactants.
I was wondering whether any one can suggest any tool or any program which can
create a 3D grid and then calculate the gaussian curvature on points on the 3D
grid .
Thanks
Hi,
Is there any tool in gromacs that can compute the fraction of native contacts
rho ( i,e the typical parameter that quantifies how close the folding
protein is to the native ) ?
Thanks
Sanku--
gmx-users mailing listgmx-users@gromacs.org
Dear Users ,
I am trying to use PLUMED with gromacs4.5.4 to perform umbrella sampling
simulation using replica exchange as implemented within gromacs. I am using
radius of gyration as the collective variable along which umbrella sampling is
being performed. However, I find that whenever I
Hi,
I am trying to use a table potential implementing Weeks-Chandler-Anderson
(WCA) interaction between a solute and all atoms of a solvent like TIP3P water
( with nonzero interaction in the Hydrogen atoms) . But, I am having a trouble
in specifying energy groups required for table potential.
Hi all,
I am trying to do an umbrella sampling of a fairly extended state of the
protein along end-to-end distance of it. I am using a rectangular box (
elongated along x ) of dimension 20 nm X 8nm X 8 nm. I am doing the simulation
in NVT ensemble. gromacs 4.5.4 is being used.
But, even
Hi,
I am trying to compute free energy of a polymer in presence of a constant
force.
If I understand correctly, I need to use two pull-option here in gromacs: one
for performing umbrella sampling and other for applying constant force. But,
as far as I know I can not specify two pull option
Hi,
Is carbohydrate forcefield in Charmm or Amber included in gromacs4.5.5
topology folders ?
Sanku
--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
Bipin,
There might be a workaround. You might want to check out Plumed plugin in
latest versions of VMD for calculating fractions of native contact. You can
load the gromacs trajectory along with the native .gro file in VMD and use
Plumed plugin inbuilt in VMD . You need to install plumed
Hi,
I am trying to compute the free energy change using g_bar: I am using
two-stage decoupling process as in Justin Lemkul's tutorial.
But , I get following warning in all cases regarding violation of second law of
thermodynamics. Can someone explain what is this error about and which lambda I
Dear Gromacs users,
I am trying to perform a MD simulation in gromacs 4.5.4 using a protein and
ligand in gas phase.
I have previously run the simulation in water without any problem. Now, I want
to compare the result to see the effect of solvent.
But for running the same simulation after
Hi,
I am trying to do implicit solvent simulation for a protein in gas-phase. I
have a few questions :
1) should I use sd integrator?
2) should I also use no periodic condition considering continuum dielectric ?
3) in the JCTC 2010 paper by Lindahl and co-worker, it is mentioned that no
Hi Erik,
That statement was a typo. The simulation will be done in implicit solvent (
not in gas phase).
Sanku
From: Erik Marklund er...@xray.bmc.uu.se
To: Sanku M msank...@yahoo.com; Discussion list for GROMACS users
gmx-users@gromacs.org
Sent: Friday
Hi,
I am recently trying to perform an umbrella sampling simulation along a
particular reaction coordinate on a system where I have also put position
restraint on certain atoms of the system... So, for each umbrella sampling
window, I have an extra potential on certain atoms ( due to the
Dear Gromacs user,
I was having a question on when need to use jacobian coorection of -2KTln(r)
( gromacs manual chapter 6) term when calculating PMF. I understand for a
3-dimensional radial coordinate like distance between two groups, this term
need to taken care of. But, if the PMF is
Hi,
I wanted to check what is actually OPLS-2005 forcefield that is recently
being referred often for md simulation. However, I also see that whenever,
OPLS-2005 is being referred, it cites a 2001 paper by Jorgensen on OPLS
forcefield. So, what is actually OPLS-2005?
So, I wonder what version
Hi,
I was looking for some way out for converting the trajectory-files back and
forth between two softwares between gromacs and Desmond.
More specifically, if I run a simulation for a particular system using gromacs
4.5.4 , how can I convert it into Desmond trajectory file format ?
Sanku--
PM
Subject: Re: [gmx-users] How to convert a gromacs trajectory to Desmond
trajectory format
On 28/10/2011 9:46 AM, Sanku M wrote:
Hi,
I was looking for some way out for converting the trajectory-files back
and forth between two softwares between gromacs and Desmond.
More specifically, if I
Hi,
When trying to compile fftw3.3.3 in our cluster I got following error.
Apparently, it try to guess the build-type by trying to create a directory in
scratch. I am not sure why it will try to create a directory there and then it
fails. I was wondering whether there is any way-out to avoid
Hi Cara,
Thanks for a very clarifying email. It helps a lot.
Sanku
From: Cara Kreck cara_...@hotmail.com
To: gmx-users@gromacs.org
Sent: Friday, October 28, 2011 3:50 AM
Subject: RE: [gmx-users] query on OPLS-2005
Hi Sanku
According to the Schrodinger
Hi,
I have a protein pdb file with ACE as N-cap and I am trying to use pdb2gmx (
within gromacs 4.5.4 ) to generate a topology file using opls/AA . the ACE is
present in opls aminoacids.rtp files. But, on issuing the pdb2gmx command, I
get following error message:
Program pdb2gmx_44, VERSION
Hi,
I just compiled gromacs 4.5.4 in a cluster. But, I find that if I try to make
use of threading introduced in gromacs 4.5.x series, it does not work.
After issuing command like mdrun -v -s , I expected that for my 8-core
processor which is not running any other jobs, the threading will
Hi,
I have done some steered MD simulation and I want to construct the potential
of mean force from these pull-profile using Jarzinsky's inequality. I wanted to
see whether, in updated version of gromacs, there is any implementation of
extracting PMF from SMD simulations.
If not, can anyone
the PMF from sMD simulations using the weighted
histogram analysis method (WHAM) in gromacs- Justin Lemkul's tutorial does a
nice job of explaining it:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html
- Laura
On 10/31/2011 11:05 AM, Sanku M wrote:
Hi,
I
Hi,
I am performing steered Molecular dynamics simulation to pull a molecule out
of a complex. I am using gromacs 4.5.4 to perform the constant rate pulling..I
have done the steered MD simulation in a particular direction i.e hav pulled
the molecule out of complex.
But, to check the
from pullf.xvg will provide the work .
Or, will it be force ( obtained from pullf.xvg) multiplied by pulling rate
multiplied by time ?
From: Justin A. Lemkul jalem...@vt.edu
To: Sanku M msank...@yahoo.com; Discussion list for GROMACS users
gmx-users@gromacs.org
from pullf.xvg will provide the work .
Or, will it be force ( obtained from pullf.xvg) multiplied by pulling rate
multiplied by time ?
From: Justin A. Lemkul jalem...@vt.edu
To: Sanku M msank...@yahoo.com; Discussion list for GROMACS users
gmx-users@gromacs.org
Hi,
I am performing steered MD simulation using gromacs.
I was wondering how one can get the time profile of the irreversible work from
the gromacs pull-code out put . From constant pulling-rate SMD, we get time
profile of force pullf.xvg and pullx.xvg. I wonder does multiplying the the
value
Did you create/have any .mdp file called 'minim.mdp' . The grompp is looking
for the run parameter file and not finding it as you may not have created one.
From: Salvatore Guccione gucci...@unict.it
To: gmx-users@gromacs.org
Sent: Saturday, November 5, 2011
Hi,
I just wanted to check whether g_wham ( in gromacs4.5.4) already subtract the
entropic contribution ( -2KTlog(r) term ) term when unbiasing the histogram
obtained from umbrella sampling using distance in 3D as a reaction coordinate.
Thanks
Sanku--
gmx-users mailing list
Hi,
I have a system containing water and a large protein. In the simulation, I do
not want the protein center of mass to drift away. I was wondering what will be
the reasonable method in gromacs to fix the position of the center of mass of
the protein in its original position . I was thinking
Hi,
I find that in the ffnonbonded.itp under OPLS forcefield ( inside opls.ff
directory), for each particle-type, there is a partial charge assigned to it.
However, again in the .rtp file, for each residue, under each charge group,
each of the atom is assigned
another partial charge assigned
Hi,
I would like to know if there is a way in gromacs to calculate the
time-averaged density of solvent which is confined between two objects , say,
two plates or another example will be water confined between ligand and
binding-pocket.
I was thinking about two ways for going about this but
Hi,
It might be a very minor issue but I find in versions of gromacs 4.5.4, the
output log file ( in verbose mode) writes the progress of the simulation in a
single line ( unlike in previous gromacs 4.0.7 version) where it used to write
the progress in a new lines. As a result, in
Hi,
This has been compiled and installed in same machine which runs Linux. It
never happens in any other version lower than gromacs4.5.
Sanku
From: Broadbent, Richard richard.broadben...@imperial.ac.uk
To: Sanku M msank...@yahoo.com; Discussion list
Hi,
I am wondering whether someone can suggest a reference paper based on which
all gromacs principal component analysis (PCA) analysis ( i.e g_covar and
g_anaeig tools) tools are based . Or, any other review articles on PCA
analysis is based will also be useful.
Thanks
Sanku--
gmx-users
Hi,
I have a technical question regarding feasibility of combining replica
exchange with umbrella sampling or any other pulling simulations in gromacs.
Since the umbrella sampling or any other pulling simulations are
non-equilibrium simulation due to presence of external bias, I wonder
Hi,
I sent this email few weeks back and thought sending it again in case someone
can give some opinion.
I have a technical question regarding feasibility of combining replica
exchange with umbrella sampling or any other pulling simulations in gromacs.
Since the umbrella sampling or any other
Hi,
I am simulating a peptide in a box of water in gromacs 4.5.4 . From the
trajectory, I want to compute the time-averaged force acting on the peptide.
I found g_traj tool can provide information on force upon supplying the
traj.trr file and g_traj help menu also suggests that using -af
Hi,
I am wondering whether there is any way in GROMACS that one can find which
groups are the main Hbonding partners in a trajectory. For example, if I
simulate a peptide in water, I want to know during the simulation, which
particular atoms in the peptides are making most of the Hbonds with
Hi,
I am trying to understand what are the angles g_sorient plans to compute.
The manual says that the theta1 is the angle with the vector from the first
atom of the solvent molecule
to the midpoint between atoms 2 and 3 . But, I wonder what is the reference
position of this angle ? In
Hi,
Is it possible in GROMACS4.5 to perform computation of relative binding free
energy of a ligand to a protein due to mutation in the ligand ( or due tio
mutation in the protein)?
I have done the computation of solvation free energy of a solute in a solvent
using FEP but looking for some
Hi,
I am using a cluster where user/local/bin has some old mpi executable. But, I
have installed openmpi-1.3 in my own home directory so that I can use that for
installing gromacs4.5.4 parallel version. I have also updated the path with the
openmpi bin directory and library directory in the
Hi,
I have run a simulation of a fixed object in water using gromacs. Now, I want
to analyze only water molecules which are present within a cylinder of certain
radius (smaller than simulation box dimension in XY plane).
I wonder whether gromacs has any particular tool which can identify the
Hi,
Is there any way in gromacs to use radius of gyration of a polymer as
reaction coordinate for umbrella sampling ?
Thanks
Sanku--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Hi,
Is there any known issue/problem in running FEP calculations with charm27.ff
in gromacs4.5.4 ? I tried running an FEP calculation using charmm27.ff by
interpolating A state and B state but it gives error that dihedral terms with
multiple values can not be interpolated..One need to write
Hi,
I am having a problem with running a NVE ( micro-canonical) ensemble using a
system of 128 Martini DPPC lipids. I started the simulation with a 128 lipid
bilayer with Martini water which was pre-equilibrated in NPT ensemble ( using
berendsen temperature coupling at 325 K( separate
Hi,
I was interested in calculating the diffusion constant of the center of mass
of entire lipid-bilayer ( not individual lipid molecules). Regarding this, I
had two doubts I wanted to clarify:
1. Since I am interested in calculating the diffusion constant of the
bilayer iteself, I guess
Hi,
I would like to use constraint force pull code to calculate the free energy
of association of two peptide using the distance between center of mass of two
peptides as reaction coordinate. I am planning to use gromacs 4.
Here I have some queries:
1. Since I will constraint method, I
Hi,
I would like to use constraint force pull code to calculate the free energy
of association of two peptide using the distance between center of mass of two
peptides as reaction coordinate. I am planning to use gromacs 4.
Here I have some queries:
1. Since I will constraint method, I
Hi,
I am trying to calculate the PMF of two peptides using constraint in gromacs
4.0.5. But, I am finding a very large oscillation( from -1000 to +1000) in the
force that is being printed in pullf.xvg file . Is this oscillation normal ? In
that case at any distance, the mean force will be
Hi,
I am planning to add an external harmonic potential along z direction of a
system : i.e U(z)= 0.5*K*z(**2)
I was wondering if I can get an help on how to add an user-defined external
potential like this in gromacs ?
Thanks
Sanku
--
gmx-users mailing listgmx-users@gromacs.org
Hi,
I am trying to write a topology in gromacs format for a recently developed
molecule in OPLS format. From the parameterization-paper, I know the partial
charges on each of the atom in that molecule from the corresponding paper .
But,
I am not sure how to split the molecule topology into
Hi,
I am interested in simulating a anionic molecule BF4(-) ( Boron
tetrafluoride). In the paper which developed the parameters for this molecule,
it is mentioned that it has been used as 'rigid' molecule i.e the molecule only
has non-bonding interaction but there was no intramolecular
, April 27, 2011 8:25:05 PM
Subject: Re: [gmx-users] rigid tetrahedral molecule
Sanku M wrote:
Hi,
I am interested in simulating a anionic molecule BF4(-) ( Boron
tetrafluoride). In the paper which developed the parameters for this
molecule,
it is mentioned that it has been used as 'rigid
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Wed, April 27, 2011 11:14:34 PM
Subject: Re: [gmx-users] rigid tetrahedral molecule
On 4/28/2011 1:54 PM, Sanku M wrote:
Hi,
I tried to keep the geometry of the BF4 fixed by using constraints
using lincs. But , unfortunately
...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Thu, April 28, 2011 1:00:42 AM
Subject: Re: [gmx-users] rigid tetrahedral molecule
On 4/28/2011 3:49 PM, Sanku M wrote:
I went through the LINCS manual . But, I am still struggling with
coming up with the idea
Hi,
I was wondering whether someone can comment on what vdw-cutoff scheme will
be
suitable when using a molecule under OPLS/AA force field . Also, providing some
details about what cut-off value one should use will be really helpful.
Thanks
Sanku--
gmx-users mailing list
to do this is left as an exercise for the reader.
I hope this helps.
best,
Gyorgy
Citando Sanku M msank...@yahoo.com:
Thanks. The molecule was developed as a part of OPLS. The authors used a
software called BOSS( developed in Bill Jorgensen's lab) . I guess this
softwares have way
Hi,
I am having a problem with trjconv to get a single snap-shot from a
trajectory
file. I am using gromacs 4.0.7 .
If I try to get a snapshot corresponding to 14 ps, I was trying to use -b 14
-e 14 command as follows. But,
If I issue this command as shown below
trjconv --f traj.xtc -o
, trajectory ended at 14'
Any help will be appreciated.
Sanku
From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Thu, May 5, 2011 10:22:38 AM
Subject: Re: [gmx-users] trjconv problem
Sanku M wrote:
Hi,
I am
I found it will work if I use -b 13.9 -e 14.1
From: Sanku M msank...@yahoo.com
To: jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Thu, May 5, 2011 10:33:19 AM
Subject: Re: [gmx-users] trjconv problem
Hi Justin,
In many
Hi,
I am planning to run replica exchange simulation using gromacs 4.0.7 . I have
read the manual about REMD. Only thing I wanted to know is that how I can
specify the name of host-machines where I am planning to run the simulations.
I have 10 different quad-core computers each
to be on the same
machine. The above approach will generally achieve that.
Mark
-- Josh
On Wed, 2011-05-25 at 11:50 -0700, Sanku M wrote:
Hi,
I am planning to run replica exchange simulation using gromacs
4.0.7 . I have read the manual about REMD. Only thing I wanted to know
Hi,
I was running a replica exchange simulation in a PBS queue which was killed
as
my simulation crossed the maximum time limit. I was planning to restart the
simulation. I am using gromacs 4.0.7
I was wondering what should be the command line arguement for the multiple
.cpt file for
Hi,
I was wondering whether Gromacs can be used to perform simulation using
Dreiding force field developed by Goddard and co-workers ( J.Phys.Chem.
,94,8897,1990). If someone can share some experience in porting this force
field
in gromacs, that will be very helpful.
Sanku--
gmx-users
Hi,
I am using gromacs_4.0.7 to calculate the Scattering Intensity as a function
of scattering vectors(q) using g_rdf -sq command .
But, I found that there is no way that one can increase/decrease the grid
spacing for structure factor calculation. I tried using -bin option , but that
does
Hi,
I am using gromacs_4.0.7 to calculate the Scattering Intensity as a function
of scattering vectors(q) using g_rdf -sq command .
But, I found that there is no way that one can increase/decrease the grid
spacing for structure factor calculation. I tried using -bin option , but that
does
Hi ,
I was wondering whether current GROMACS versions can perform transition path
sampling to study rare events ?
Sanku
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Hi,
I wanted to run an atomistic simulation where I would like to constrain
helicity of a helical peptide( i.e the initial configuration is an ideal helix)
. I was wondering whether there is a way to constrain the helix dihedral angles
in Gromacs. Also, if there is any other option to keep
Hi,
I am trying to calculate the dipole-dipole interaction energy of two charged
molecules. But, I was looking for a method/formula to do that. I have the .xtc
file from which I can calculate the dipole moment of each of the molecule using
g_dipole . But, then how will I calculate the
Hi,
I am trying to use trjorder command to generate a sorted trajectory where all
the water molecules are certain distance away. I can use the trjorder command
to
generate the sorted trajectory where all waters are sorted based on distance
but
I am looking for method for creating a index
Hi,
Occasionally I hear that one need to use WHAM( weighed histogram analysis)
method in collaboration with Temperature-Replica exchange simulation. But, I
was not understanding why one need to use WHAM with temperature-remd
simulation.
Can someone explain me ?
Does one need to use any
Hi ,
I am planning to calculate the residence time of a counter-ion near the
charged head group of surfactant. I was wondering whether some one can suggest
how one can calculate residence time in gromacs?
Thanks
Sanku--
gmx-users mailing listgmx-users@gromacs.org
is the residence time. Is it ?
Sanku
From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tue, July 12, 2011 9:13:20 PM
Subject: Re: [gmx-users] residence time calculation
Sanku M wrote:
Hi ,
I am planning
Hi,
I am running a replica exchange simulation using 64 replicas ( using
gromacs4.0.7) in a super computer using 2 nodes ( each having 32 processors).
But, what happens is that after running for a day or so, the simulation crashes
with error like 'XTC error, may be you are out of quota'. But,
Hi,
I am running a simulation where I have 100 chains of molecule in a box . I am
trying to calculate the distance between two particular atoms ( present in each
molecule) averaged over all the chains of molecule. i.e If I have atom C1 and
C2 in each of the molecule-chain, I want to
Hi,
I was wondering whether, in gromacs, there is any way of calculating the
electrostatic free energy using poisson Boltzmann equation.
Sanku--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Hi,
I was planning to do some analysis by reading in a XTC file using Fortran code
. I was wondering what is the best possible option I can have .
Sanku--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Hi,
I was planning to use Thermodynamic integration to calculate solvation free
energy of a molecule in a solvent. I was following Justin Lemkul's online
tutorial.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html
. I found that
a) a sd
Hi,
I was wondering whether in gromacs 4, one can use replica exchange simulation
in combination with umbrella sampling.
Thanks
Sanku--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Hi,
I am trying to calculate the solvation free energy using thermodynamic
integration(TI) method . I am using gromacs 4.0.7 . But, I am having a problem
in getting accurate average temperature .
The following is what I did:
I found that when doing TI, grompp recommends using 'sd' (
-users@gromacs.org
Sent: Tue, August 2, 2011 8:08:20 PM
Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP
Sanku M wrote:
Hi,
I am trying to calculate the solvation free energy using thermodynamic
integration(TI) method . I am using gromacs 4.0.7 . But, I am having
: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tue, August 2, 2011 8:26:16 PM
Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP
Justin A. Lemkul wrote:
Sanku M wrote:
Hi Justin,
I first performed two
: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tue, August 2, 2011 8:40:21 PM
Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP
Sanku M wrote:
Hi Justin,
So, do you suggest that after minimization, I should
: [gmx-users] Problem with temperature and stochastic dynamics in FEP
Sanku M wrote:
OKK, But, before, I have tried using md as integrator where I start the
initial
velocity as 280K ( which makes sense as the minimized configuration is
essentially at low temperature) and have used Nose-hoover
as time-step.
From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tue, August 2, 2011 10:16:17 PM
Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP
Sanku M wrote:
Hi Justin
From: Mark Abraham mark.abra...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tue, August 2, 2011 11:46:21 PM
Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP
On 3/08/2011 2:23 PM, Sanku M wrote:
Finally, I
with temperature and stochastic dynamics in FEP
On 4/08/2011 1:51 AM, Sanku M wrote:
Hi Mark and Justin,
I did investigate on the rvdw=rlist issue. But, I found even if I
make rvdw rlist and still keep time step 0.002, the average
temperature goes to 303 K.
Only reducing the time step
Hi,
I was using gromacs 4.0.7 to calculate the scattering intensity of polymer
solvated in a solvent. But, I found a discrepancy in the normalization of the
calculation when considering only a subset
of the entire system ( e.g . only solute from the entire solution) :
This is what I found:
Hi,
I was wondering whether hamiltonian replica exchange simulation has been
implemented in latest version of gromacs . Or, is there any other way of
performing the hamiltonian replica exchange using some variants of
lambda-dynamics ?
Sanku--
gmx-users mailing listgmx-users@gromacs.org
Hi,
I was wondering whether hamiltonian replica exchange simulation has been
implemented in latest version of gromacs . Or, is there any other way of
performing the hamiltonian replica exchange using some variants of
lambda-dynamics ?
Sanku--
gmx-users mailing listgmx-users@gromacs.org
Hi,
Does anyone know about availability of MM pair-wise additive forcefield for
thiocyanate anion ( SCN- ) , either in CHARMM or OPLS format ?
Sanku--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Hi,
I am trying to calculate the density profile of head group of bilayer normal
to z direction using gromacs 4.0.7. I was trying to center the density profile
about dx/2.dy/2,0 . But, I am finding problem with using center option. I find
using -center option does not shift the bilayer to
Hi,
I was wondering whether BD simulation integrator in Gromacs also have option
of including hydrodynamic interactions.
Sanku--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
simulation.
From: Sanku M msank...@yahoo.com
To: Dommert Florian domm...@icp.uni-stuttgart.de
Sent: Monday, September 26, 2011 6:07 AM
Subject: Re: [gmx-users] BD with Hydrodynamic interactions?
I did not mean lattice boltzmann by BD.
By BD I meant Brownian Dynamics
Hi,
I am having a problem in a cluster which is IBM PowerPC 970MPs and running
SUSE linux and it has IBM XL C Fortran compliers ( xlf, xlc ).
I was trying to install gromacs 4 there using open-mpi which is already
installed using ibm compilers.
Here is my configure command:
./configure
Hi,
I have run a simulation using gromacs 4.0.7 with 50 copies of amphiphilic
surfactant ( in water) using Martini coarse-grained force-field. Mere
visualization of trajectories shows that starting with 50 discrete copies, they
gradually aggregate and finally two well-separated large micelles
Hi,
I am trying to estimate the solvent accessible surface area of hydrophobic
tails of a martini DPPC lipid bilayer . I was going to use g_sas for that.
But, I observe that this tool gets the vanderwal radii from vdwradii.dat file.
But, since the particles in the martini lipids are
Hi,
I was trying to use g_rdf to calculate radial distribution function g(r)
between lipid tails and a peptide close to membrane. What I find is that the
g(r) never goes to 1 at long distance. It is less than 1 at long distance .
My general question is : Is it always necessary that g(r)
Dear gromacs users,
I was planning to study the interaction of a peptide with a zinc
oxide ( ZnO) surface. So, I was wondering whether there is any forcefield for
metal oxide especially for Zinc Oxide ( ZnO) in literarure that you can suggest
that can be used in combination with
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