Hello everyone,
This question may be very simple to most of the Gromacs user. I wonder if
Gromacs allow us to use both user-defined non-bonded potentials (Table
potential) as well as Gromacs predefined potential at the same time. For
example, if I have a system with a solute in a solvent and for
s
Add the -sep flag that will split the writting into multiple files instead of 1
large pdb. Alternatively you could script up a spliting program with something
like awk
awk 'BEGIN{filename="MyFile_"i".pdb"}{print $0>filename; if $0~/ENDMDL/;
i++;filename="MyFile_"i".pdb"}}'
-Micholas
===
Hi,
I want to do some tests on the lysozyme tutorial. Assume that the tutorial with
the default parameters which is run for 10ps, takes X seconds wall clock time.
If I want to increase the wall clock time, I can simply run for 100ps. However,
that is not what I want.
I want to increase the amoun
You could compile Gromacs with PLUMED (http://www.plumed.org/) and use
that to run your umbrella sampling with replica exchange.
-Marc
On Thu, Mar 8, 2018 at 11:32 AM, Mayank Dixit
wrote:
> Dear Gromacs Users,
> I would like to calculate the potential of mean force between sodium and
> chlorid
OK thank you Justin for the confirmation
Stéphane
--
On 3/9/18 6:55 AM, ABEL Stephane wrote:
> Dear all,
>
> I am constructing a top file for gramicidin A a short that contains a
> succession of D- and L-AAs (the exact sequence is
> HCO-L-Val-D-Gly-L-Ala-D-Leu-L-Ala
Dear director,I am using Gromacs package to perform MD simulations and I have a
100 ns long MD simulation. For the further assays, I must split this 100 ns
trajectory into 100 pdb files (to get one pdf file from each 1000 ps or 1 ns of
simulation).
I have found two commands:
gmx trjconv -s to
Hi Mayank,
Umbrella sampling replica exchange is currently not implemented in GROMACS.
--
Viveca
On Thu, Mar 8, 2018 at 5:32 PM, Mayank Dixit
wrote:
> Dear Gromacs Users,
> I would like to calculate the potential of mean force between sodium and
> chloride ion pair in water using replica exch
On 3/9/18 4:43 AM, Neda Rafiee wrote:
Dear users,
I want to calculate Phenyl dipole moment from my traj.trr file but my
trajectory does not contain mass and charge.
Trajectories never have mass and charge; those are fixed aspects of a
system and are therefore in the topology (.tpr file).
On 3/9/18 6:55 AM, ABEL Stephane wrote:
Dear all,
I am constructing a top file for gramicidin A a short that contains a succession
of D- and L-AAs (the exact sequence is
HCO-L-Val-D-Gly-L-Ala-D-Leu-L-Ala-D-Val-L-Val-D-Val-L-Trp-D-Leu-X-D-Leu-L-Trp-D-Leu-L-Trp-NH-CH2-CH2-OH)
and have a unexp
Dear all,
I am constructing a top file for gramicidin A a short that contains a
succession of D- and L-AAs (the exact sequence is
HCO-L-Val-D-Gly-L-Ala-D-Leu-L-Ala-D-Val-L-Val-D-Val-L-Trp-D-Leu-X-D-Leu-L-Trp-D-Leu-L-Trp-NH-CH2-CH2-OH)
and have a unexpected problem whenI use charmm36 . Indeed
Dear director,This is Mansoureh Shahbazi, a Ph.D. candidate in medical
biotechnology at Pasteur Institute of Iran. I am using Gromacs package to
perform MD simulations in my thesis and I have a 100 ns long MD simulation. For
the further assays, I must split this 100 ns trajectory into 100 pdb f
Dear users,
I want to calculate Phenyl dipole moment from my traj.trr file but my
trajectory does not contain mass and charge. I used "gmx dipole " command for
this purpose but it gives me error that Phenyl is not a whole molecule
(actually because it is part of my protein which is a molecule i
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