Hello everyone, I'm trying to perform REMD simulation at NPT emsemble.
Here I have some question.
1) Using parrinello-rahman pressure coupling, REMD simulation is unstable at
high temperature.
(highest temperature ~400K).
2) Using berendsen T-coupling and P-coupling scheme..(tau_t =
hi, Justin. Thank you for your meticulous and patient explanation !
Before I see this post, I misunderstood the meaning of sharing bonds.
I thought note only the bonds,but also the angles and the dihedrals
should be added to top file.
It was so complicated to deal manually that I wrote that
Hi,
I am running a coarse-grained simulation of a lipid vesicle (~70,000
particles), using a rhombic dodecahedron box to limit the amount of
solvent I require. The vesicle (unsurprisingly) moves over the periodic
boundaries during the simulation. Various analyses I am conducting
require
Thanks. I see MOPAC7 is in the public domain. That way I can use it on
my project!
1 The original copyright notice of MOPAC7:
2
3 C
4 C Notice of Public Domain nature of MOPAC
5 C
6 C 'This computer program is a work of the United States
7 C
Mark Abraham ha scritto:
Sorry, I was a bit incomplete last night. Charge groups are the
fundamental unit for neighbour-searching (3.4.2) to construct lists of
charge groups for nonbonded interactions, which determine lists of
atom-atom interactions. However, the nonbonded interactions are
hema dhevi wrote:
hi justin,
thanks for your reply
Totally I have 6126 atoms (residues + DPPC ) I am using the same pdb file
and lipid pdb (DPPC-128) which is given in the KAPL tutorial.
OK, just to clarify - are you working on the actual KALP tutorial when this
error comes up, or are
Hello,
I tried using the amber force field in GROMACS. I proceeded as follows:
Determined my parameters with RED/ANTECHAMBER/tleap converted them with
amb2gmx.pl
(or with acpypi, problem is the same) to gromacs coordinate and topology files.
It concerns a modified nucleotide. I minimized with
Hello,
My name is Pieter van 't Hof. As part of my Master thesis in computer
science I am currently extending Gromacs and VMD to visualize short
range Lennard Jones potentials and Coulomb forces during interactive
molecular dynamics simulations. In order to choose a representation
method which is
Hello,
My name is Pieter van 't Hof. As part of my Master thesis in computer
science I am currently extending Gromacs and VMD to visualize short
range Lennard Jones potentials and Coulomb forces during interactive
molecular dynamics simulations. In order to choose a representation
method which is
This looks like more of a pymbar question!
I am trying to calculate free energy of a system that involves
disappearance of LJ particle at lambda=1 in explicit solvent. I ran the
simulation at 20 different lambda points ranging from 0 to 1, using soft
core potential. In order to use MBAR
Hi:
This is to ask how to proceed to minimize a CG ensemble made of a
transmembrane multimer with pore region immersed in a hydrated DPPC
bilayer and extracellular region immersed in water. Total height 18
nm, width 10 nm in the extracellular region and 6 nm in the pore
region. No clashes/contacts
Francesco Pietra wrote:
Hi:
This is to ask how to proceed to minimize a CG ensemble made of a
transmembrane multimer with pore region immersed in a hydrated DPPC
bilayer and extracellular region immersed in water. Total height 18
nm, width 10 nm in the extracellular region and 6 nm in the pore
I am using Gromacs on windows hen executing pdb2gmx command, I got an error
i.e.
Fatal error: Atom HD1 in residue HISB 3 not found in rtp entry with 14 atoms
while sorting atoms. May be different protonation state. Remove this
hydrogen or choose a different protonation state.
I want to know what
Hi,
I got a problem with the output structure files (gro/trr/xtc) generated by the
energy minimization with GROMACS 4. That is, when I used the generated
structure as the input for further minimizations or MD simulations, I got very
large potential energy and forces at step 0, as if the
Hi,
Thanks for the suggestion to use trjconv -pbc nojump. Unfortunately, it
has not worked, as the vesicle is still not whole in the trajectory. I
have tried subsequently centering the trajectory, and representing the
system with -ur compact, but still it does not work. I am wondering if
the
Ni Hao,
You don't give too much information here. What exactly are you doing?
What are the commands? What's the difference between the first and the
second pass of EM? One thing to check is whether the output/input file
has a correct box definition.
Cheers,
Tsjerk
2009/11/30 HAO JIANG
Hi Daniel,
If the structure is correct in the coordinate file you used as input
to generate the .tpr, you can use that structure as reference to
trjconv, using -pbc nojump.
Cheers,
Tsjerk
On Mon, Nov 30, 2009 at 6:17 PM, Daniel Parton
daniel.par...@bioch.ox.ac.uk wrote:
Hi,
Thanks for the
pawan raghav wrote:
I am using Gromacs on windows hen executing pdb2gmx command, I got an
error i.e.
Fatal error: Atom HD1 in residue HISB 3 not found in rtp entry with 14
atoms while sorting atoms. May be different protonation state. Remove
this hydrogen or choose a different protonation
Francesco Pietra wrote:
Failed to specify that both the DPPC bilayer and the box of water are
from equilibrated systems in MARTIN web, while the protein was Amber
minimized (and MD) before generating the CG.
I have tried the cg protein alone
genbox -cp my.pdb -box 15 -o my.gro
Again I ask
servaas wrote:
Hello,
I tried using the amber force field in GROMACS. I proceeded as follows:
Determined my parameters with RED/ANTECHAMBER/tleap converted them with amb2gmx.pl
(or with acpypi, problem is the same) to gromacs coordinate and topology files. It concerns a modified nucleotide. I
ms wrote:
Mark Abraham ha scritto:
Sorry, I was a bit incomplete last night. Charge groups are the
fundamental unit for neighbour-searching (3.4.2) to construct lists of
charge groups for nonbonded interactions, which determine lists of
atom-atom interactions. However, the nonbonded
On Mon, Nov 30, 2009 at 8:18 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Francesco Pietra wrote:
Failed to specify that both the DPPC bilayer and the box of water are
from equilibrated systems in MARTIN web, while the protein was Amber
minimized (and MD) before generating the CG.
I have
Tsjerk,
Thanks for your reply.
I am doing a simple test case with 500 SPC/E water molecules. First I did
minimization with steepest decent, using a command like
mdrun -pd -s water.gro.tpr -c final.gro
The generated md.log looks like the following:
Step
Francesco Pietra wrote:
On Mon, Nov 30, 2009 at 8:18 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Francesco Pietra wrote:
Failed to specify that both the DPPC bilayer and the box of water are
from equilibrated systems in MARTIN web, while the protein was Amber
minimized (and MD) before
Justin A. Lemkul wrote:
Then that's certainly the first problem to fix. This is why I generally
use editconf for defining the box (and why I keep recommending it). For
a simple protein in water, using a command like:
editconf -c -d 1.0
will define a suitably-sized box so that you don't
Hi,
Is it possible in GROMACS to extract from trajectory file 9 components of
tensor of inertia moments at each time step? I know that it is possible to
extract 3 vectors, but not whole tensor. Any suggestions?
Thank you
Egis
--- On Tue, 12/1/09, gmx-users-requ...@gromacs.org
mrshi...@gmail.com wrote:
What other input might you need for a test set? As a minor developer and
a stickler for accuracy, I would be very much interested in the sorts of
inputs your looking for, and have some ideas as well.
There's a number of issues listed in the posts in the URLs below,
Hi Daniel,
I think you still need to read and attempt what has already been
suggested. To be more explicit:
trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster
grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr
trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump
from:
Dear Gromacs users,
my system consist of two parts, which are not connected. My system has around
10 atoms. To make the trajectory handling and the analysis more feasible I
store only the CA atoms in the xtc trajectory.
I want to use the g_mindist command to calculate the minimal distance
Hi List,
I have downloaded topolbuild1.2.1 but cannot extract files. Can anyone help
and check the link?
Many thanks
--
Regards,
Neha Gandhi Gajaria,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845
--
gmx-users mailing list
Hi,
trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster
You might want to use -dump to extract a specific frame, rather than using -e:
trjconv -f a.xtc -o a_cluster.gro -pbc cluster -dump 0
Also, do mind that for a subsequent call to trjconv, using -pbc nojump
and the extracted frame as
hai justin,ya i am working on actual KALP tutorial
onlyhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmxtutorials/membraneprotein/index.htmland
i am using the pdb file which is given in the website. This is the first time
i am doing MD simulation for transmembrane proteins before
hai justin,ya i am working on actual KALP tutorial
onlyhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmxtutorials/membraneprotein/index.htmland
i am using the pdb file which is given in the website. This is the first time
i am doing MD simulation for transmembrane proteins before
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