I did simulation of protein-dna complex in water solvent. After
simulation, two strands of dna was separated when I displayed my a.xtc
with VMD.I used (trjconv –f a.xtc –s a.tpr –n a.ndx –o b.xtc –pbc
nojump) and problem fixed. But now I have another problem. Before using
–pbc nojump, there wer
On 2010-10-27 09.40, David van der Spoel wrote:
I did simulation of protein-dna complex in water solvent. After
simulation, two strands of dna was separated when I displayed my a.xtc
with VMD.I used (trjconv –f a.xtc –s a.tpr –n a.ndx –o b.xtc –pbc
nojump) and problem fixed. But now I have ano
Hi,
with the nojump option, your water molecules will slowly
diffuse out of the "home" box and appear far away from your
protein if you display the MD system with VMD or pymol.
You can split your trajectory in two parts (using index groups)
and use different options on them individually:
a) on th
Hi Carsten
Thanks for your answer. You got my case very well.
I understand your mean as follows:
1) Trjconv –f a.xtc –s a.tpr –o b.xtc –pbc mol (output group=water)
2) Trjconv –f a.xtc –s a.tpr –o c.xtc –pbc nojump (output group
=protein-dna)
Is that true?
You said, (Then over
On Oct 27, 2010, at 10:05 AM, leila karami wrote:
> Hi Carsten
>
> Thanks for your answer. You got my case very well.
>
> I understand your mean as follows:
>
> 1) Trjconv –f a.xtc –s a.tpr –o b.xtc –pbc mol (output group=water)
>
> 2) Trjconv –f a.xtc –s a.tpr –o c.xtc –pbc noju
Hi Leila,
Maybe you're better off trying:
1. trjconv -pbc nojump # choose system for output
2. trjconv -center -pbc mol # choose protein/dna for centering, system
for output
Centering is done before removing PBC, so you should be safe with two passes.
You might also want to play with -ur t
Dear Tsjerk
I did what you said:
1. trjconv -f a.xtc -s a.tpr -o 1.xtc -pbc nojump (system for output)
2. trjconv -f a.xtc -s a.tpr -o 2.xtc -pbc mol –center (pr/dna
for centering, system for output)
Now, I need new trajectory file for analysis. How I obtain new
trajectory file fr
Dear Carsten and David and Tsjerk
Thanks for your time and attention
My purpose of these questions is to find a way that 1) close two separated
strand of dna (in my case only –pbc nojump fix it) and also 2) water
molecules to be put in interface of between protein and dna. Because I want
to sur
add dihedral parameter for you EPON molecule.
Check this:
http://oldwww.gromacs.org/pipermail/gmx-users/2005-May/015044.html
2010/10/24 英雄不再寂寞
> Dear gmxers,
> I try to simulate a complex system using gmx-4.5.1. I have carried out
> the minimization without any errors, but when it comes to
Carla Jamous wrote:
Hi Justin,
I guess the problem is in the way I concatenate my trajectory.
So my question may seem stupid but I can't seem to understand this part
of the manual:
c (continue) - The start time is taken from the end
of the previous file. Use it when your continuation run
re
Hi Leila,
2.xtc should contain all that you want.
My point was that you shouldn't need to separate protein/dna and
solvent into two trajectories to be combined later.
Note that this only concerns visualization. You can do distance and
H-bond calculations on the original trajectory, as the relevant
Dear Tsjerk
Thus, as you said, Xtc file obtained from trjconv –pbc nojump only concerns
visualization. Thus, can I use old xtc file (with out –pbc nojump) for
analysis such as interfacial waters and water mediated hydrogen bonds or
every other analysis?
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Hi everyone,
please is there a way to know if electrostatic interactions exist between my
ligand and my protein during the trajectory? Which tool can I use for this
purpose, other than g_saltbr?
Thank you,
Carla
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Right :)
On Wed, Oct 27, 2010 at 2:27 PM, leila karami wrote:
> Dear Tsjerk
>
> Thus, as you said, Xtc file obtained from trjconv –pbc nojump only concerns
> visualization. Thus, can I use old xtc file (with out –pbc nojump) for
> analysis such as interfacial waters and water mediated hydrogen bo
Bert,
instead of directly answering your question, let me suggest that you
don't want to pull in absolute coordinates. Probably, you want to pull
your polymer with respect to the position of some other (non-water)
reference group. The only reason that I can think of to use absolute
coordi
Carla Jamous wrote:
Hi everyone,
please is there a way to know if electrostatic interactions exist
between my ligand and my protein during the trajectory? Which tool can I
use for this purpose, other than g_saltbr?
You can quantify short-range nonbonded energies using energygrps, which at
Hi,
While using trjconv I get this error:
VMD_PLUGIN_PATH not set. Using default location:
/usr/local/lib/vmd/plugins/*/molfile
No VMD Plugins found
Set the environment variable VMD_PLUGIN_PATH to the molfile folder within
the
VMD installation.
The architecture (e.g. 32bit versus 64bit) of Groma
Sai Pooja wrote:
Hi,
While using trjconv I get this error:
VMD_PLUGIN_PATH not set. Using default location:
/usr/local/lib/vmd/plugins/*/molfile
No VMD Plugins found
Set the environment variable VMD_PLUGIN_PATH to the molfile folder
within the
VMD installation.
The architecture (e.g. 32
Dear all
I am including the parameter for the Zinc in the topology file all the bonded
and nonbonded parameters have been included in the topology still it is not
accepting the parameter the Zn atom move away from the coordination.
Thanking you in advance
E R Azhagiya singam
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gmx-users m
babu gokul wrote:
Dear all
I am including the parameter for the Zinc in the topology file all the
bonded and nonbonded parameters have been included in the topology still
it is not accepting the parameter the Zn atom move away from the
coordination.
Have you actually specified bonds betw
Hi,
I was planning to simulate a system of long-chain alkane carboxylate in
water
with a chemical formula CH3-(CH2)_20-COOH .
For that I was thinking of using an united atom force-field. I found , in
gromacs, there are two United atom force-field available: GROMOS-96 and
OPLS-UA.
I was wo
Hello,
I am trying to calculate the viscosity of my pure water system at 275K. The
system has run for 40ns. I issued the following command:
g_energy_d_mpi -f 275K_50_50_50_2.edr -s 275K_50_50_50_2.tpr -nmol 4202 -vis
sixsitewater_275K -b 0 -e 4
The numbers I get in the output file are
Hi all,
I have been following the method outlined by Yuguang Mu to generate the
energy landscape along two eigenvectors. There are four minima that I wish
to explore. I can determine the points along the vectors that correspond to
the conformation, but am unsure of how to use those to obtain the
co
Ali Naqvi wrote:
Hi all,
I have been following the method outlined by Yuguang Mu to generate the
energy landscape along two eigenvectors. There are four minima that I
wish to explore. I can determine the points along the vectors that
correspond to the conformation, but am unsure of how to us
Check the original specifications for each of those force fields, then
check to see if the molecule you are wanting to simulate falls within
the boundaries of how the force field was derived. Also search the
literature for simulations of the same or similar molecules, and see
which force fields th
I am getting the following warning message from g_rama, even for a simple
system like a blocked Alanine dipeptide:
$ g_rama -s test.tpr -f traj.xtc
[…]
Reading file test.tpr, VERSION 4.5.1 (single precision)
Found 1 phi-psi combinations
Dihedral around 6,8 not found in topology. Using mult=3
[…]
>
> Yes I have been using the how-to for making the energy landscape. Now I
> just need to go backwards.
>
> Ali Naqvi wrote:
> > Hi all,
> > I have been following the method outlined by Yuguang Mu to generate the
> > energy landscape along two eigenvectors. There are four minima that I
> > wish to
Please keep all Gromacs-related correspondence on the gmx-users list. I am not
a private tutor. I am CC'ing the list on this message; I would ask that you
post anything further there.
To solve your problem, please see the following document:
http://www.gromacs.org/Downloads/Installation_In
Dear GMX users,
I have a problem when I run gromacs-4.5.1 on a cluster, I can only do
paralleled running using 1 node, which is 8-cpu, but when I use more nodes, it
will abort abnormally. Could someone help me figure it out? Thanks very much!
All the best,
fancy
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gmx-users mailing list
On October 28, 2010 at 4:05 AM fancy2012 wrote:
Dear GMX users,
I have a problem when I run gromacs-4.5.1 on a cluster, I can only do paralleled running using 1 node, wh
On October 28, 2010 at 4:11 AM TJ Mustard wrote:
On October 28, 2010 at 4:05 AM fancy2012 wrote:
Dear GMX users,
Can't help you directly, other than suggestion you provide a lot more
information than you have. Direct copy/paste of the command lines used,
error messages and log files generated, how GROMACS was installed etc.
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institut
fancy2012 wrote:
Dear GMX users,
I have a problem when I run gromacs-4.5.1 on a cluster, I can only do
paralleled running using 1 node, which is 8-cpu, but when I use more
nodes, it will abort abnormally. Could someone help me figure it out?
Thanks very much!
To get a faster resolution
Dear GMX users,
Now, I am doing some simulations about ionic liquids. The
problem I am encountering is how to check the equilibrium of Ionic liquid
system. The boss asks me to do the RSMD to check it, but I think it is not
right. Could you give me some useful advice?
Thank you very mu
On 28/10/2010 3:03 AM, Sai Pooja wrote:
Hi Mark,
I am familiar with the section, however, I have a few doubts.
When you say ...
So modified protein-water VDW interactions can be introduced by
defining all relevant "protein atom"-"TIP3P oxygen" [nonbond_params]
terms.
Do you mean that I can intr
On 28/10/2010 2:24 AM, Nilesh Dhumal wrote:
Thanks a lot.
I made some changes in topology file for rerun simulation.
Still I am getting same potential energy.
If topology files are different then why the potential energy is same?
Occam's razor says that the topologies are not (meaningfully) dif
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