Dear all
Is it possible to save trajectories in gromacs not at constant frequency
but at a logarithmic frequency?
Jagannath
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Dear Gromacs users and developers
Is there any new update on implementation of constant pH simulations on
recent gromacs version?
I am aware of the gromacs faq
http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation
But I wanted to check if there is any update on this ?
Jagannath
--
Dear Gromacs-users
I need to compute the time profile of number of water away from a
membrane center along z direction. However trjorder -nshell -r 0.6 will
give me the number of waters along radial direction.
there is an option in trjorder -z . but that just orders molecule along
z. but does
give us any early access, in practice. We have some cards, but
> perhaps no actual run until early next week.
>
> Mark
>
> On Fri, 27 May 2016 18:22 Jagannath Mondal <jmondal.bac...@gmail.com>
> wrote:
>
> > Dear Gromacs users
> >
> > I just wanted to
give us any early access, in practice. We have some cards, but
> perhaps no actual run until early next week.
>
> Mark
>
> On Fri, 27 May 2016 18:22 Jagannath Mondal <jmondal.bac...@gmail.com>
> wrote:
>
> > Dear Gromacs users
> >
> > I just wanted to
Hi
My installation of gromacs_5.0.6 is not working at 'make' stage in
ubuntu. The same machine had no problem in installing the same version
earlier.
I am having following issues near the completion of 'make' stage:
Any help will be appreciated.
[100%] *Linking CXX executable
Dear Mark
Did you have a chance to test gromacs with GTX 1080? Can you please let
us know if it is compatible and working well.
Jagannath
On Sat, May 28, 2016 at 2:36 PM, Jagannath Mondal <jmondal.bac...@gmail.com>
wrote:
> Dear Mark
>
>I will appreciate if you share your e
. NVIDIA didn't
> manage to give us any early access, in practice. We have some cards, but
> perhaps no actual run until early next week.
>
> Mark
>
> On Fri, 27 May 2016 18:22 Jagannath Mondal <jmondal.bac...@gmail.com>
> wrote:
>
> > Dear Gromacs users
> >
Dear Gromacs users
I just wanted to check whether latest GPU of NVIDIA GTX 1080 has been
tested by any one for its compatibility/performance with gromacs.
I have used GTX 980 Ti and have found it compatible with gromacs with a
significant performance boosting. I wanted to check if the latest
Hi
I am also interested in the issue of using a flat-bottomed restraint,
for a spherocylinder.
However, I am not sure whether the current gromacs settings of even a
linear combination of a sphere and cylinder can help here to generate a
spherocylinder.
If we put the spherical and cylindrical
Hi
I am also interested in the issue of using a flat-bottomed restraint,
for a spherocylinder.
However, I am not sure whether the current gromacs settings of even a
linear combination of a sphere and cylinder can help here to generate a
spherocylinder.
If we put the spherical and cylindrical
Hi
I have to impose a spherocylindrical confinement on the particles I am
currently performing simulation with.
For that I will appreciate your feedback/comments regarding two of my plans:
1. I was mainly looking at flat-bottomed potential option within gromacs
to see if it can be used to
for flat-bottomed potential withing gromacs 5.x installation directory?
On Sat, Sep 12, 2015 at 7:52 AM, Barnett, James W <jbarn...@tulane.edu>
wrote:
> On Fri, 2015-09-11 at 11:57 +0530, Jagannath Mondal wrote:
> > Hi
> > I would like to perform a simulation ( without any
for flat-bottomed potential withing gromacs 5.x installation
directory?
Thanks
Jagannath
On Sat, Sep 12, 2015 at 7:52 AM, Barnett, James W <jbarn...@tulane.edu>
wrote:
> On Fri, 2015-09-11 at 11:57 +0530, Jagannath Mondal wrote:
> > Hi
> > I would like to perform a simulation (
Dear gromacs-users
I have a system of protein-ligand system. I would like to use different
color for ligand location at different time-frame. The final goal is to
have a snapshot where ligand location of all time frame are color-coded
using a color-gradient ( for example : red at short time and
uch better performance with
> some compilers than others.
>
> --
> Szilárd
>
> On Tue, Mar 15, 2016 at 2:18 PM, jagannath mondal <jm3...@columbia.edu>
> wrote:
>
> > Dear Gromacs users
> > I am trying to perform Free energy peturbation calculation in presence
Dear Gromacs users
I am trying to perform Free energy peturbation calculation in presence of
distance, angle and dihedral-restraint for a protein-ligand system.
However, I am finding, on turning on the FEP calculation, the performance
of gromacs5.1.1. in a gpu-based workstation significantly
> Cheers,
>
> Tsjerk
> On Mar 8, 2016 06:50, "Jagannath Mondal" <jmondal.bac...@gmail.com> wrote:
>
> > Dear gromacs-users
> >
> > I am sorry to write you a visualization-related query. I hope you can
> > help.
> >
> > My query is: How ca
Dear gromacs-users
I am sorry to write you a visualization-related query. I hope you can
help.
My query is: How can I visualize a trajectory file ( example in vmd) where
I have an extra 4th column ( apart from x y z which are first 3 columns)
which has a dynamically changing variable for each
2016 at 10:10 PM, Tsjerk Wassenaar <tsje...@gmail.com>
wrote:
> Hi Jagannath,
>
> Backward actually can do both. For conversion of a Gromos system use
>
> backward.py -from gromos -to martini
>
> Hope it helps,
>
> Tsjerk
>
>
> On Mon, Feb 29, 2016 at 11:
6 at 10:10 PM, Tsjerk Wassenaar <tsje...@gmail.com>
wrote:
> Hi Jagannath,
>
> Backward actually can do both. For conversion of a Gromos system use
>
> backward.py -from gromos -to martini
>
> Hope it helps,
>
> Tsjerk
>
>
> On Mon, Feb 29, 2016 at 11:
Dear Tsjerk
I had a similar question. I guess insane.py script is supposed to build a
coarse-grained membrane/solvent system from scratch. But, if I already have
a particular existing atomistic configuration of lipid/water system along
with some proteins ( which I had obtained by performing an
Dear Tsjerk
I had a similar question. I guess insane.py script is supposed to build a
coarse-grained membrane/solvent system from scratch. But, if I already have
a particular existing atomistic configuration of lipid/water system along
with some proteins ( which I had obtained by performing an
Dear Gromacs/Martini-users
I wanted to transform a snapshot of my atomistic DPPG/water bilayer to the
Martini coarse-grained format. However, I found martinize.py script does
not transform lipid or waters to coarse-grained counterpart.It only works
for protein. So, Is there any particular way I
Dear Users
I want to compute the relative free energy for mutating one residue of a
protein to another one using free energy perturbations as implemented in
gromacs. I wanted to know how I can generate the starting configurations of
the intermediate lambda values. Is there any interpolation
Hi
Previously, with gromacs 4.5.4, I had not experienced any problem with
freeze group in NPT ensemble . However, in gromacs 5.0, the same simulation
is crashing. Any suggestion regarding what is best setup for freeze group
calculation in NPT ensemble in gromacs 5.x
Jagannath
--
Gromacs Users
for the graphene size I am interested in.
Jagannath
On Fri, Jan 15, 2016 at 6:14 AM, VITALY V. CHABAN <vvcha...@gmail.com>
wrote:
> The force constants were either from OPLS or from AMBER (which of these is
> referenced in the paper?)
>
>
>
> On Thu, Jan 14, 2016 at 5:40 P
Dear Gromacs users
I wanted to calculate PMF of association of two graphene plates using
umbrella sampling simulations. However, my concern is how we can maintain
the planer configuration of two plates along xy-planes while performing the
umbrella sampling along the separation along z
Dear all
Is there a tool or method to generate coordinates of a model beta sheet
structure for a given sequence ?
Jagannath
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Hi
I need to do a simulation of protein in presence of LiBr salt solution.
However, I am not finding any force field parameters for bromide ion either
in charmm forcefields or amber forcefields. Can someone suggest a decent
source for bromide ion forcefield parameters that one could employ in
Hi
I would like to perform a simulation ( without any periodic boundary
condition) where I need to have a wall of spherocylindrical geometry. In
other words the particles will be confined inside a spherocylinder.
Is there any good suggestion on how to achieve that in gromacs?
1) One option I
Dear Gromacs Users
I am trying to run gpu version of gromacs5.0.6 in a work-station which is
a hexacore processor that can be multithreaded to 12. The workstation has 2
Geforce GT 610 GPUs . I am finding the simulation using -nb gpu is
exceedingly slower than -nb cpu ( i,e turning off gpu)
I
wrote:
> Hi Jagannath,
>
> AFAIK GT610's are rather slow. What you could try is using both cpu and
> gpu for non-bonded interactions (-nb gpu_cpu)
>
> Peter
>
> On 04/09/15 15:01, jagannath mondal wrote:
> > Dear Gromacs Users
> >
> > I am trying to r
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