On 9/07/2011 3:20 AM, Marcelo A. Carignano wrote:
Thank you Mark.
On Jul 8, 2011, at 11:17 AM, Mark Abraham wrote:
On 9/07/2011 1:36 AM, Marcelo A. Carignano wrote:
Hi all,
Stochastic dynamics is described in section 3.8 of the Manual (v. 4.5)
Equation 3.108 is dimensionally incorrect, or at
On 9/07/2011 3:37 AM, raghu...@bcpindia.org wrote:
Hi
I have a problem related to submitting a mdrun job on cluster. I
tried to ask help or gromacs and rocks users-group.
My machine specs.
Cluster of Intel Xeon processors:QC with Rocks Cluster. 8 processors
(16 threads)
When I submit md
E. Nihal Korkmaz wrote:
Dear all,
I am trying to solvate a protein in a dodecahedron box, and the box
doesn't seem right. I tried /trjconv -s ur compact -pbc mol, /that
ended up with a dodecahedron shaped water distrubution around the
protein however the box is still shown as triclinic inb
Dear all,
I am trying to solvate a protein in a dodecahedron box, and the box doesn't
seem right. I tried *trjconv -s ur compact -pbc mol, *that ended up with a
dodecahedron shaped water distrubution around the protein however the box is
still shown as triclinic inbn Pymol? Is this Pymol's weakne
Eric Fiedler wrote:
In g-cluster
Fatal error:
Error: too many iterations in routine JACOBI
I don't even know where to start with this one.
There are many reasons why this may occur. Search the list archive for
possibilities:
http://www.gromacs.org/Support/Mailing_Lists/Search
If you'r
In g-cluster
Fatal error:
Error: too many iterations in routine JACOBI
I don't even know where to start with this one.
-Eric
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailin
Fixed!
Thank you!
On Jul 8, 2011, at 3:23 PM, Justin A. Lemkul wrote:
>
>
> Eric Fiedler wrote:
>> Hi,
>> I'm running Gromacs 4.5.1. Our group uses lammps for our simulations, but I'm
>> trying to use the g_cluster tool. I used VMD to convert trajectory files to
>> .trr and .pdb format, then a
Eric Fiedler wrote:
Hi,
I'm running Gromacs 4.5.1. Our group uses lammps for our simulations, but I'm
trying to use the g_cluster tool. I used VMD to convert trajectory files to
.trr and .pdb format, then attempt to run g_cluster using:
g_cluster -f traj.pdb -s trajstart.trr -g cluster.log -c
Hi,
I'm running Gromacs 4.5.1. Our group uses lammps for our simulations, but I'm
trying to use the g_cluster tool. I used VMD to convert trajectory files to
.trr and .pdb format, then attempt to run g_cluster using:
g_cluster -f traj.pdb -s trajstart.trr -g cluster.log -cutoff 1 -fit -method
errabah fatima ezzahra wrote:
two trimers , the first that has three peptides , first pepetide goes
from N to C terminus and the other are antiparallel with it they go from
C to N so if you look at the end of peptides on one side of the first
trimer you see LEU GLU GLU
then the other trim
two trimers , the first that has three peptides , first pepetide goes from N
to C terminus and the other are antiparallel with it they go from C to N so if
you look at the end of peptides on one side of the first trimer you see LEU GLU
GLU
then the other trimer that is one goes from N-ter
errabah fatima ezzahra wrote:
Hi All
I am using course grained model where i have the whole glutamic acid as
a sphere , and the other end is Lucine (hydrophobic) , do i need to
still worry about capping the residue to evoid the negative charge in
GLU from repelling other GLU .
Capping g
Hi
I have a problem related to submitting a mdrun job on cluster. I tried
to ask help or gromacs and rocks users-group.
My machine specs.
Cluster of Intel Xeon processors:QC with Rocks Cluster. 8 processors
(16 threads)
When I submit mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px
p
Hi All
I am using course grained model where i have the whole glutamic acid as a
sphere , and the other end is Lucine (hydrophobic) , do i need to still worry
about capping the residue to evoid the negative charge in GLU from repelling
other GLU .
Also is it possible to control the orientati
Thank you Mark.
On Jul 8, 2011, at 11:17 AM, Mark Abraham wrote:
On 9/07/2011 1:36 AM, Marcelo A. Carignano wrote:
Hi all,
Stochastic dynamics is described in section 3.8 of the Manual (v.
4.5)
Equation 3.108 is dimensionally incorrect, or at least I cannot
understand it.
Left hand side
On 9/07/2011 1:36 AM, Marcelo A. Carignano wrote:
Hi all,
Stochastic dynamics is described in section 3.8 of the Manual (v. 4.5)
Equation 3.108 is dimensionally incorrect, or at least I cannot
understand it.
Left hand side is a force,
Specifically, mass * length * time^-2. Note that (d^2 r)/
Hi all,
Stochastic dynamics is described in section 3.8 of the Manual (v. 4.5)
Equation 3.108 is dimensionally incorrect, or at least I cannot
understand it.
Left hand side is a force, and the first term on the right hand side
has a missing length in the numerator to be a force.
This is accor
On 6/07/2011 5:55 AM, Juliette N. wrote:
Hello Dear all,
I have a few short questions about pressure coupling settings, namely
isothermal compressibility. I hope you can guide me.
A) By default gmx is taking the value for water but I was wondering if
this has to be modified for other systems
On 8/07/2011 11:06 PM, raghav singh wrote:
Hi Justin, All,
This is my recent log of PDB2GMX command... I have got what I wanted
but I would really appreciate if one you experts have a look and let
me know weather everything is fine.
I have not calculated new charge distribution after removin
t; ====
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/P
I think so!
2011/7/8 Szilárd Páll :
> I think you made the right decision! :)
> --
> Szilárd
>
>
>
> On Fri, Jul 8, 2011 at 12:50 PM, Андрей Гончар wrote:
>> Thanks a lot!
>> Now we decided to use gromacs under linux and the installation of
>> gromacs and gromacs-gpu has passed without errors
>>
I think you made the right decision! :)
--
Szilárd
On Fri, Jul 8, 2011 at 12:50 PM, Андрей Гончар wrote:
> Thanks a lot!
> Now we decided to use gromacs under linux and the installation of
> gromacs and gromacs-gpu has passed without errors
> Problem is solved :)
>
> 2011/7/8 Szilárd Páll :
>>
Thanks a lot!
Now we decided to use gromacs under linux and the installation of
gromacs and gromacs-gpu has passed without errors
Problem is solved :)
2011/7/8 Szilárd Páll :
> Well, unfortunately I don't know of any step-by-step tutorial, but
> from what I remember the workflow is pretty straight
On Fri, 8 Jul 2011 13:07:56 +0530
manoj gadhwal wrote:
> Hello to all,
>I am using the Gromacs 4.5.3 in Centos-5 and I
> need the xmgrace or Grace for plotting the graph for output file .
> But when I tried to install grace by the option *'yum install
> grace*', there was no f
shiva birgani wrote:
shiva birgani wrote:
> Dear Justin
> I have prepared the pdb structure of an organic compound.
> This compound is applied as a lable which covalently and specifically
> attaches to a Cys residue of our protein.
> I want to attache the label to the protein and simulate
shiva birgani wrote:
> Dear Justin
> I have prepared the pdb structure of an organic compound.
> This compound is applied as a lable which covalently and specifically
> attaches to a Cys residue of our protein.
> I want to attache the label to the protein and simulate this complex.
> what I need to
This is what I mean by "quick and dirty".
#!/bin/bash
# Reads the output of "g_sas" per residue (-or) and writes only the residues
you want.
# Diego E.B. Gomes, Roberto D. Lins, Pedro G. Pascutti, Thereza A. Soares
# mailto: di...@biof.ufrj.br
#1 ) To perform multiple g_sas (will write out
Sir,
You are right..I exactly mean the same as you interpretednow I am clear.
Thanks a lot for your reply...
On Fri, Jul 8, 2011 at 13:26, felmer...@uchile.cl wrote:
> Hey,
>
> I agree it was unclear, but i guess he meant that he has a crystal
> structure with two molecules in the asymmetric u
On 8/07/2011 6:35 PM, manoj gadhwal wrote:
Hello to all,
I am using the Gromacs 4.5.3 in Centos-5. When I
tried to open the/*.xvg*/ file by gnuplot it shown the error. I am
attaching the gnuplot error and the data of .xvg file. It show that
line 9:invalid character. Please h
Hi,
in gnuplot first you must neglect the lines starting with @ # &
gnuplot> set datafile commentschars "#@&"
then you can plot the xvg file
and
On 07/08/2011 10:35 AM, manoj gadhwal wrote:
Hello to all,
�� I am using the Gromacs 4.5.3 in Centos-5. When I tried to
open the/
Hello to all,
I am using the Gromacs 4.5.3 in Centos-5. When I tried to
open the* .xvg* file by gnuplot it shown the error. I am attaching the
gnuplot error and the data of .xvg file. It show that line 9:invalid
character. Please help me.
Thanks in advance.
*
gnuplot error:*
gn
Hey,
I agree it was unclear, but i guess he meant that he has a crystal structure
with two molecules in the asymmetric unit where he knows that the protein is a
monomer in solution. Otherwise the question does not even make sense as you
pointed out.
If it is indeed the asymmetric unit thing, t
On 8/07/2011 5:37 PM, manoj gadhwal wrote:
Hello to all,
I am using the Gromacs 4.5.3 in Centos-5 and I need
the xmgrace or Grace for plotting the graph for output file . But when
I tried to install grace by the option */'yum install grace/*', there
was no file to install. a
On 8/07/2011 4:52 PM, bipin singh wrote:
Hello,
My protein have two identical chains A and B and the backbone rmsd
between the two chains is 0.33A.
My problem is that how to select(on what basis) one chain out of the
two for md simulation, whether the selection of one of the two
chains(A or B
Hello to all,
I am using the Gromacs 4.5.3 in Centos-5 and I need the
xmgrace or Grace for plotting the graph for output file . But when I tried
to install grace by the option *'yum install grace*', there was no file to
install. and I am not able to install properly by the grace
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