Hi,
Did grompp warn you that your time step was too large for a system without
constraints? What did you do about that?
Mark
On Thu, 24 Mar 2016 00:28 abhishek khetan wrote:
> Dear gmxers,
>
> I've been tryin to simulate ion-pairing in non-aqueous solvents. I first
> did the energy of the pure
Dear gmxers,
I've been tryin to simulate ion-pairing in non-aqueous solvents. I first
did the energy of the pure solvent box without any dynamics and
minimization to emtol= 10 and noticed that the last details of the system
were:
Energies (kJ/mol)
Bond Angle Ryckaert-Bell.
Hi,
Or probably gmx traj -s -f -n -ox will write an index group from a
trajectory to an .xvg text file. But generally one should consider other
ways to handle raw coordinates.
Mark
On Wed, Mar 23, 2016 at 7:19 PM Justin Lemkul wrote:
>
>
> On 3/23/16 2:15 PM, Athina Meletiou wrote:
> > Hello a
On 3/23/16 1:42 PM, gozde ergin wrote:
Hi everybody,
I would like o run ammonium sulphate solution with CHARMM force field in
GROMACS.
pdb2gmx is not working because the residue type is LIG.
I tried to use swissparam and paramchem website however both do not support the
inorganic sulphate an
On 3/23/16 2:15 PM, Athina Meletiou wrote:
Hello all,
I've been wondering if there is a way to convert a Gromacs xtc trajectory to a
plain text file. I've tried Openbabel as it appears to be possible but
unfortunately it crashes without a warning. Is there maybe a Gromacs tool that
can do t
Hello all,
I've been wondering if there is a way to convert a Gromacs xtc trajectory to a
plain text file. I've tried Openbabel as it appears to be possible but
unfortunately it crashes without a warning. Is there maybe a Gromacs tool that
can do the conversion?
Also, as I'm interested in writ
Hi everybody,
I would like o run ammonium sulphate solution with CHARMM force field in
GROMACS.
pdb2gmx is not working because the residue type is LIG.
I tried to use swissparam and paramchem website however both do not support the
inorganic sulphate and ammonium explicitly.
Is there any other e
Hi Irem,
The correction vectors is internal bookkeeping stuff, making sure to keep
track of what is where in a computationally efficient manner.
To get rid of this, I think the best option is to rotate your unit cell, to
have the largest vector (your third) along the x-axis. The second largest
sh
Hi,
There’s been a small update on my unit cell problem. To recap the issue: I am
trying to simulate a protein in its unit cell with water. The protein has the
following unit cell dimensions: a=25.036, b= 29.410, c= 52.794, alpha= 89.45,
beta= 86.29, gamma= 82.39. When I try to run energy min
1) I guess Langevins used as thermostat works good as some kind of
imitation of thermal motion produced by collisions of atoms with
virtual particles in case when we modify tau_t depending of what kind
of system we simulate e,g protein in water or in membrane. Why such
algorithm produce wrong dynam
Hmm, the first one ends the abstract with
"Correct dynamical properties, at least those studied in this paper, are
obtained with the Berendsen thermostat applied globally, despite the fact
that it yields the wrong kinetic energy distribution."
So what does (un)physical mean in this respect, in re
Hi,
e.g. http://pubs.acs.org/doi/abs/10.1021/ct400109a and
http://pubs.acs.org/doi/abs/10.1021/ct300688p
Mark
On Wed, Mar 23, 2016 at 12:00 PM Xavier Periole wrote:
>
> Any reference to illustrate the unphysical behavior of macromolecular
> systems using Berendsen thermostat compare to others?
Any reference to illustrate the unphysical behavior of macromolecular systems
using Berendsen thermostat compare to others?
XAvier.
> On Mar 23, 2016, at 10:42, James Starlight wrote:
>
> Btw taking back to my question regarding thermostats in CG sims- does
> the correct choise influence on
Hi,
Nobody advocates the use of Berendsen coupling in production simulation.
But it does not follow that one can only use langevin dynamics to be
accurate - mdrun implements several other coupling approaches...
Mark
On Wed, 23 Mar 2016 10:43 James Starlight wrote:
> Btw taking back to my quest
Hi Mark,
Thank you for the advice and the journal article! I'm studying the paper
now.
Best,
Jernej
On Wed, Mar 23, 2016 at 5:26 PM <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:
> Send gromacs.org_gmx-users mailing list submissions to
> gromacs.org_gmx-users@maillist.sys.
Btw taking back to my question regarding thermostats in CG sims- does
the correct choise influence on sampling here`? E.g in full atomistic
sims generally langevens dynamics produces better results in
comparison to berendsen thermostat which produce very unphysical
behaviour for the macromolecular
Hi Mark,
In combination with the time step and maybe the particle mass, that would
be lovely. A dynamic update, based on the actual displacements would also
be possible after some steps (-rdd -1 ?).
Cheers,
Tsjerk
On Mar 23, 2016 09:37, "Mark Abraham" wrote:
> Hi,
>
> Tsjerk, does it make sens
Hi,
You should take a look at
http://onlinelibrary.wiley.com/doi/10.1002/jcc.24030/abstract for
background information.
On Wed, Mar 23, 2016 at 6:28 AM Jernej Zidar wrote:
> Hi,
> Recently I received a dual Xeon ( 2x E5-2630v3) workstation with two
> Tesla K40c cards.
>
> I'm now trying to
OK, I will try now!
May the error be related to big shift of the receptor within thw
membrane plane due to the tranlational diffusion7
I made vizualization of the trajectory in VMD and observed relatively
big motion of the protein within membrane plane due to the tendency of
the oligomerization of
Dear all
I have installed gromacs on cygwin 64 bit computer and it has installed
successfully but when i run the command -pdb2gmx.exe following error occued
C:/cygwin64/usr/local/gromacs/bin/pdb2gmx.exe: error while loading shared
libraries: cyggmxpreprocess-6.dll: cannot open shared object file:
Hi,
Tsjerk, does it make sense to try to have grompp observe the particle
density and guide the default of -rdd accordingly?
Mark
On Wed, Mar 23, 2016 at 9:19 AM Tsjerk Wassenaar wrote:
> Hi James,
>
> Try setting -rdd 1.4 in mdrun. Sometimes 1.5 or 1.6 is necessary
> (especially if you use a
Hi,
Don't know - we don't really support a Cygwin build any more. But you might
need to source GMXRC properly, per install guide, or do a statically linked
build of GROMACS.
Mark
On Wed, Mar 23, 2016 at 9:30 AM tasneem kausar
wrote:
> Dear all
> I have installed gromacs-5.1.2 in cygwin 64 bit
Dear all
I have installed gromacs-5.1.2 in cygwin 64 bit computer. cmake have
finished successfully during installation. While executing the command
"cygcheck /usr/local/gromacs/bin/pdb2gmx.exe" it gives following error-
cygcheck: track_down: could not find cyggmx-6.dll
cygcheck: track_down: cou
Hi James,
Try setting -rdd 1.4 in mdrun. Sometimes 1.5 or 1.6 is necessary
(especially if you use a larger time step, like 30 fs).
Cheers,
Tsjerk
On Mar 23, 2016 09:08, "James Starlight" wrote:
> Hello,
>
>
> I am trying to perform 2 MARTINI simulations of several membrane
> receptors within m
Hello,
I am trying to perform 2 MARTINI simulations of several membrane
receptors within membrane i) with eldyn restrains applied on the
protein tetriary structure and ii) unrestrained md. I have no problems
in the i) case but in the ii) my simulation is very unstable under
pruduction run- it beg
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