Dear All,
I want to
ask some questions about trajectory analysis. I have some md simulation output
files that includes coordinate, force and velocity information. And these files
are huge ( more than 5 GB ) . Could you please recommend a free text editor
which
works on Linux or Windows to open
On 30/05/2012 4:45 PM, oguz gurbulak wrote:
Dear All,
I want to ask some questions about trajectory analysis. I have some md
simulation output files that includes coordinate, force and velocity
information. And these files are huge ( more than 5 GB ) . Could you
please recommend a free text
Hi All,
I have to use the long range correction for VDW, in fact i used cut-off=1.4 nm
for calculation of surface tension of TIP4P/2005, we can get 65 dyn. The .mdp i
used are as follow, I really need to know how to get a surface tension of 69.5
dyn for TIP4P/2005 water model. Becasue my
On 30/05/2012 5:33 PM, MD wrote:
Hi All,
I have to use the long range correction for VDW, in fact i used
cut-off=1.4 nm for calculation of surface tension of TIP4P/2005, we
can get 65 dyn. The .mdp i used are as follow, I really need to know
how to get a surface tension of 69.5 dyn for
Hello,
I am currently analyzing a bunch of trajectories and one thing I am doing
is to use g_sas to generate the average and standard deviation per residue.
The resulting xvg file should be formatted for use with xmgrace but I do
not seem to be able to get the standard deviation in the graph. I
Yes, i try to get a surface tension of 69 dyn, but i can only get 65 at present.
Yes, i tried some arbitrary choices. I do not know what is the correct .mdp for
me to get a surface tension of 69. May be for this version, it does not include
this function
Thanks for your kind message. But i
On 30/05/2012 7:24 PM, MD wrote:
Yes, i try to get a surface tension of 69 dyn, but i can only get 65
at present.
Yes, i tried some arbitrary choices. I do not know what is the correct
.mdp for me to get a surface tension of 69. May be for this version,
it does not include this function
Hello everyone,
As a follow up to my message last week regarding the addition of
phospholipid (PC, PE, PG and Cardiolipin) topologies to the Lipidbook
website, I am happy to announce that we have also added parameters for
lipid A from E. coli. Lipid A is the lipidic component of
Hi,
I do not know, how TIP4P/2005 has been parametrized, but the VdW cutoff
you are using is quite large. Did the authors of TIP4P/2005 really
applied this large cutoff ? This is very important, because the force
field is always parameterised in respect to certain parameters and vdW
is an
On 5/30/12 4:58 AM, Marc Hömberger wrote:
Hello,
I am currently analyzing a bunch of trajectories and one thing I am doing is to
use g_sas to generate the average and standard deviation per residue. The
resulting xvg file should be formatted for use with xmgrace but I do not seem to
be able
Hi all,
I want to set the lowest point in my curve as zero instead of negative
number. Can anyone tell me which option to use to do that?
--
Regards,
Nitin Agrawal,
Master's Student (Bioinformatics)
University of Turku,Finland
B.Tech (Biotechnology)
National Institute of
On 5/30/12 6:29 AM, Nitin Agrawal wrote:
Hi all,
I want to set the lowest point in my curve as zero instead of negative number.
Can anyone tell me which option to use to do that?
Set the desired value with -zprof0.
-Justin
--
Justin A. Lemkul,
Thank you
On Wed, May 30, 2012 at 1:39 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 5/30/12 6:29 AM, Nitin Agrawal wrote:
Hi all,
I want to set the lowest point in my curve as zero instead of negative
number.
Can anyone tell me which option to use to do that?
Set the desired value
hi,
recently while working on gromacs i came across this error There is
a dangling bond at at least one of the terminal ends and the force field
does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb
file. i tried to edit .tdb file by giving the terminal entries but its
On 30/05/2012 9:30 PM, ramaraju801 wrote:
hi,
recently while working on gromacs i came across this error There is
a dangling bond at at least one of the terminal ends and the force field
does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb
file. i tried to edit .tdb file
Hi Justin,
Thanks for getting back and posting the links.
On 5/29/12 6:22 AM, Stephen Cox wrote:
Hi,
I'm running a number of energy minimizations on a clathrate supercell
and I get
quite significantly different values for the total energy depending on
the
number of mpi processes /
Hi,
when I try the mentioned method for the GROMACs output (xvg file,
supposedly formatted for use with xmgrace) I am unable to print the
standarddeviation. I f I select the XYDY method it just ignores it and
plots again an XY graph.
What I then did: I stripped the file so that only residue
On 30/05/2012 9:42 PM, Stephen Cox wrote:
Hi Justin,
Thanks for getting back and posting the links.
On 5/29/12 6:22 AM, Stephen Cox wrote:
Hi,
I'm running a number of energy minimizations on a clathrate
supercell and I get
quite significantly different values for
On 5/30/12 7:42 AM, Stephen Cox wrote:
Hi Justin,
Thanks for getting back and posting the links.
On 5/29/12 6:22 AM, Stephen Cox wrote:
Hi,
I'm running a number of energy minimizations on a clathrate supercell and
I get
quite significantly different values
When I am using the command -zprof0. it is not giving the desired result. I
am using it as
g_wham -b 5000 -zprof0 -6.0 -it tpr_files.dat -if pullf_files.dat -o
profile_new1.xvg -hist histo_new1.xvg -unit kCal
but the lowest point in the graph is still -6.0 in the y axis and not set
to 0.0
Am i
On 5/30/12 8:18 AM, Nitin Agrawal wrote:
When I am using the command -zprof0. it is not giving the desired result. I am
using it as
g_wham -b 5000 -zprof0 -6.0 -it tpr_files.dat -if pullf_files.dat -o
profile_new1.xvg -hist histo_new1.xvg -unit kCal
but the lowest point in the graph is
How can I define the value at y axis then? Is there any way to bring the
y-axis value down to 0?
On Wed, May 30, 2012 at 3:24 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 5/30/12 8:18 AM, Nitin Agrawal wrote:
When I am using the command -zprof0. it is not giving the desired result.
I am
On 5/30/12 8:57 AM, Nitin Agrawal wrote:
How can I define the value at y axis then? Is there any way to bring the y-axis
value down to 0?
You want the energy minimum to be equal to zero, correct? This is nothing more
than a reference point, so the value passed to -zprof0 is the coordinate
On 5/30/12 7:47 AM, Marc Hömberger wrote:
Hi,
when I try the mentioned method for the GROMACs output (xvg file, supposedly
formatted for use with xmgrace) I am unable to print the standarddeviation. I f
I select the XYDY method it just ignores it and plots again an XY graph.
What I then did:
On 5/30/12 9:17 AM, Nitin Agrawal wrote:
I got this by using the command :
g_wham -b 5000 -zprof0 -2.0 -it tpr_files.dat -if pullf_files.dat -o
profile_new1.xvg -hist histo_new1.xvg -unit kCal
is their any way to shift the 0 in the y axis so it corresponds to -2 in the
x-axis. It is just to
Ok, Thank you once again.
On Wed, May 30, 2012 at 4:20 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 5/30/12 9:17 AM, Nitin Agrawal wrote:
I got this by using the command :
g_wham -b 5000 -zprof0 -2.0 -it tpr_files.dat -if pullf_files.dat -o
profile_new1.xvg -hist histo_new1.xvg -unit
On Tue, May 29, 2012 at 1:22 PM, Stephen Cox stephen.cox...@ucl.ac.uk wrote:
I'm running a number of energy minimizations on a clathrate supercell and I
get quite significantly different values for the total energy depending on
the number of mpi processes / number of threads I use.
You are
After creating a box using editconf and then solvating using genbox, I try to
add ions and get the infamous number of coordinates in .gro does not match
number of coordinates in topology error.
What's strange is that it only seems to happen when I am using the OPLS force
field. I can type the
On 5/30/12 11:32 AM, patrick wintrode wrote:
After creating a box using editconf and then solvating using genbox, I try to
add ions and get the infamous number of coordinates in .gro does not match
number of coordinates in topology error.
What's strange is that it only seems to happen when I
:
http://lists.gromacs.org/pipermail/gmx-users/attachments/20120530/a4ed4a18/attachment-0001.html
--
Message: 2
Date: Wed, 30 May 2012 07:51:02 -0400
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Re: Possible bug: energy changes with the
number
my fault, when i ran gromacs to produce topology file for a nucleotide
sequence it is showing the above error There is a dangling bond at at least
one of the terminal ends and the force field
does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb
file. i tried giving the starting
Hi Gromacs list,
I would like to study two different mutations in a protein molecule,
perhaps using MD.
One of them is a insert deletion and the other is a mutation to Cys
beside an existing Cys.
The problem is that most of the molecular modeling programs, including
Rosetta, do not handle with
You might be able to use MODELLER for generating the helix deletions since
it is alignment-based. If you use automodel.make(exit_stage=2) it will
generate coordinates based on the specified sequence-spatial alignment but
will stop there (otherwise it will try to run simulated annealing in
Dear Users ,
I am trying to use PLUMED with gromacs4.5.4 to perform umbrella sampling
simulation using replica exchange as implemented within gromacs. I am using
radius of gyration as the collective variable along which umbrella sampling is
being performed. However, I find that whenever I
Dear Gromacs Users,
I am trying to find out the relative free energy difference of binding of a
ligand with wild type protein (Glutamate residue) and mutant protein
(Alanine residue).
For charge part of the mutation, this is what I'm planning to do:
; residue 40 GLU rtp GLU q -1.0
552
Hi Peter,
Thanks for helping. I might not have been clear. The cys mutation is in
a different location of the indel.
I'm particularly worried about how the molecular modelling programs will
treat indels. Several things can
happen upon deletion of an helix residue. In this context, just take the
Hi,
I have a system in a slab geometry. A surface exists at z = 0; many
hydrogens protrude from the surface, and these hydrogens are mostly (but not
precisely) immobile. Above the surface, there is liquid, including the
anion BF4- (tetrahedral arrangement of fluorines around a central boron).
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