Hi, Mark,
I reduce the length of test runs to only 6 steps now. The binary identical
continuation still cannot be obtained. I use gmxcheck to compare the results
according to your suggestions and I find two reasons to cause different
trajectories.
One is a water molecule happening to
Dear users,
I want to place the peptide above aqueous phase of the bilayer.I have
gone throught the mailing list and read the manual also, but since am
a beginner to gromacs it will be very helpful if someone could mail me
the commands to insert peptide above bilayer.I understood that it can
be
Hi,
Setting
epsilon_r = 0
in your mdp file will turn off all electrostatics.
If you are concerned about efficiency, you should set all charges
in your topology to zero.
Berk
Date: Tue, 24 Feb 2009 09:49:25 +0200
Subject: Re: [gmx-users] Turning off electrostatic or Van der Waals
Hi,
pull_pbcatom is indeed a global atom index.
I will add this information to the mdp description.
I don't see how any atom number would not be affected by reordering your
topology,
except if you are thinking of group that consist of exactly one molecule.
But pull_pbcatom does not have to be
Dear all,
I want torun SO3- form that is oxidation of cys in protein (SH -- SO3-).
When I used pdb2gmx, SO3-'s atom type didn't define.
Please, does anyone have experince with SO3- and can point me to reasonable parameter.
thanks for any comment
Jin Hee
Jin Hee wrote:
Dear all,
I want to run SO3- form that is oxidation of cys in protein (SH -- SO3-).
It probably is SO3 2- or HSO3- (note that crystallography does not
detect hydrogens).
You will have to search the literature for this one...
When I used pdb2gmx, SO3-'s atom type
Thanks!
2009/2/24 Berk Hess g...@hotmail.com
Hi,
Setting
epsilon_r = 0
in your mdp file will turn off all electrostatics.
If you are concerned about efficiency, you should set all charges
in your topology to zero.
Berk
--
Date: Tue, 24 Feb 2009 09:49:25
Hi,
Are you running NPT, single processor with 4.0.3?
Then you are experiencing the bug that the box is not updated in the checkpoint
file.
Please change to 4.0.4.
Berk
From: gu...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] About the binary identical continuation by
Hi,
I have a quick question about interpreting the output from g_hbond. I am using
the -ac option to calculate H-bond lifetimes between my protein and a series of
different, bound ligands. I read the associated paper, but I would like to
confirm the interpretation of the results before I
Hi,
I would like to use nMolDyn for the analysis of the GROMACS trajectories.
I tried VMD and catdcd to convert trr/tpr files to dcd/pdb files. But the
conversion of the dcd/pdb files to nc (netcdf) files using the dcd_to_nc
program of the nMolDyn package does not work. Obviously the header of
Dear all,
I ran a 1ns simulation in SW water (polarizable model) under NPT (P=1 bar ,
T=300 K) conditions.
I checked the density and had a constant plateau value around 640 g/L , which
is obviously too low.
I used the flexible and rigid version (520 solvent molecules), with isotropic
Thank you Berk,
I did not realize that one might want to use a pull_pbcatom that is
not part of the pull_group. In that case it makes sense that it should
remain a global atom index. My comment regarding being affected by
reordering the topology was indeed poorly constructed. What I meant
Sang-Min Park wrote:
Dear all,
I ran a 1ns simulation in SW water (polarizable model) under NPT (P=1 bar ,
T=300 K) conditions.
I checked the density and had a constant plateau value around 640 g/L , which
is obviously too low.
I used the flexible and rigid version (520 solvent
On Tue, Feb 24, 2009 at 9:44 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Hi,
I have a quick question about interpreting the output from g_hbond. I am
using the -ac option to calculate H-bond lifetimes between my protein and a
series of different, bound ligands. I read the associated
Hello David,
thank you for your response.
Yes, this is the right mdp file.
The total system contains also a small NMA molecule (6 atoms), which
should not affect significantly the density (520 solvent molecules).
Sang Min
On Tue, 24 Feb 2009, David van der Spoel wrote:
Sang-Min Park
Justin A. Lemkul wrote:
Hi,
I have a quick question about interpreting the output from g_hbond. I
am using the -ac option to calculate H-bond lifetimes between my protein
and a series of different, bound ligands. I read the associated paper,
but I would like to confirm the interpretation
Sang-Min Park wrote:
Hello David,
thank you for your response.
Yes, this is the right mdp file.
The total system contains also a small NMA molecule (6 atoms), which
should not affect significantly the density (520 solvent molecules).
Sang Min
OK, I suggest that if you can reproduce the
Hi David,
I ran also a system with NMA+SPC,NMA+SPCE and other models, but the
density was always reasonable (around 1 Kg/L).
I used hereby the version 3.3.1. and all simulations were done in double
precision including the simulations with SW water.
I will also install the newer version 4.x
Manik Mayur wrote:
On Tue, Feb 24, 2009 at 9:44 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Hi,
I have a quick question about interpreting the output from g_hbond.
I am using the -ac option to calculate H-bond lifetimes between my
protein and a
David van der Spoel wrote:
Justin A. Lemkul wrote:
Hi,
I have a quick question about interpreting the output from g_hbond. I
am using the -ac option to calculate H-bond lifetimes between my
protein and a series of different, bound ligands. I read the
associated paper, but I would like
Dear all
I'm trying to measure the bending modulus (Kc) of lipid bilayer. I've
found some papers, showing that spectral intensity needs to be
calculated using the wave vector q. This method has been applied
directly for pure membrane, or for bilayers with cholesterol.
In my simulations, there is
Hi, all!
I have a question about interpreting the output from a GROMACS tool, g_sorient.
I'm analising the solvent orientation around some specific atoms of my
molecules, using GROMACS 3.3.3.
I have read the mailing lists, but I could not find anything specific about it
(although the
Hi,
I change to Gromacs 4.0.4 now, and perform NPT with four CPU cores. The results
of continuation runs are still different from the undivided run. Neither
phenomenon described previously disappears.
Guang-Jun
From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE:
GuoGuangjun wrote:
Hi,
I change to Gromacs 4.0.4 now, and perform NPT with four CPU cores.
The results of continuation runs are still different from the undivided
run. Neither phenomenon described previously disappears.
The first phenomenon is a non-problem. The files are identical
Does anybody have the topology files for ATP and/or ADP for the OPLS-AA
forcefield?. If not, how can I parameterize this molecules?.
Best regards.
Lucio Montero.
Lucio Ricardo Montero Valenzuela
Instituto de Biotecnologia, UNAM
Departamento de Biologia Molecular de Plantas
Av. Universidad
Hi,
Did you redo the run you continued from as well with 4.0.4?
Also there are two other issues that can prevent binary identical contiuation:
dynamic load balancing and FFT optimization (when using PME with fftw).
Dynamic load balancing can be turned off with mdrun -dlb no
You can turn off
Justin A. Lemkul wrote:
David van der Spoel wrote:
Justin A. Lemkul wrote:
Hi,
I have a quick question about interpreting the output from g_hbond.
I am using the -ac option to calculate H-bond lifetimes between my
protein and a series of different, bound ligands. I read the
associated
Dear all,
I have a surface in xy plane. I want to use g_density to calcuate the density
profile of solvent along z axis. As my surface groups is not homogeneuously
distributed on the surface, some parts are hydrophilic and some parts are
hydrophobic. therefore I need to divide the surface
Dear GMX-users and developers,
I am interested in doing simulation of ibuprofen (NSAIDs Drug). But I am facing
some difficulties in getting the right topologies ( OPLS-AA force field). I get
my pdb field from PRODRG server.
Does anyone can help me in getting the correct file?
Any comments
Dear all,
I am doing a protein simulation for 20ns in single processor machine. after
11.1ns when I am trying to rerun mdrun its coming out with the following
error.
--
Inner product between old and new vector = 0.0!
constraint #0 atoms 1 and 2
Warning: 1-4
hi gmx-users,
I have run g_spatial and got a *.cube output file. But I don't know how to
convert the *.cube file to a (x,y,z) format file in order to load it into other
plot software. Any suggetion is appreciated
Jinyao Wang
wan...@ciac.jl.cn
2009-02-25
Dear Gromacs users,
I am using Gromacs vs 3.3.3 on Open Suse LInux with ffG43a1 force
field. My molecule contain aromatic carbon-chlorine bond, and i want to
assign bond type for this but there is no entry in ffG43a1bon.itp correspond
to aromatic carbon-chlorine bond. I got Force constant
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