Mark Abraham wrote:
It's 5, actually, there are cross-bond-bond and cross-bond-angle
functions at 3 and 4, neither of which make it into Table 5.4. You can
see this working in the source code of src/gmxlib/ifunc.c.
The advantage of actually using this function type is that you get a
separat
Title: functionalized surface: counter ions ? PME or RF
Hello everyone,
I would appreciate some advice on my simulation.
The System is a Protein attached to a small Functionalized Surface
composed of ~250 positive carboxyl groups. The hole system is about
220,000 atoms. (amber,tip3p)
Th
Diego Enry wrote:
Hello everyone,
I would appreciate some advice on my simulation.
The System is a Protein attached to a small Funcionalized Surface
composed of ~250 positive carboxyl groups. The hole system is about
220,000 atoms. (amber,tip3p)
The big concern is how to deal with a net charge o
chiloo Laohpongspaisan wrote:
Dear all,
i have got the abnormal values of torsion angle by using g_angle of gromacs.
g_angle -f whole.xtc -s md.tpr -n index.ndx -ov out_avrg.xvg -od
out_dist.xvg -type dihedral
i use such tool in many systems, the torsions along time seem to be
normal exce
chiloo Laohpongspaisan wrote:
Dear all,
i have got the abnormal values of torsion angle by using g_angle of gromacs.
Anyone knows my problem, suggest me please.
theta + n*360 is equivalent to theta
Otherwise they look like they're varying around +/- 120 degrees which is
normal for (say)
Dear all, i have got the abnormal values of torsion angle by using g_angle of gromacs. g_angle -f whole.xtc -s md.tpr -n index.ndx -ov out_avrg.xvg -od out_dist.xvg -type dihedral i use such tool in many systems, the torsions along time seem to be normal except one. And the values are as below. 0
David van der Spoel wrote:
Jerome Henin wrote:
On Wednesday 16 August 2006 23:43, Mark Abraham wrote:
Jerome Henin wrote:
Hi all,
As quite a few people have done before, I am about to try and convert a
CHARMM topology into a GROMACS one. To that effect, I will probably
need
one or severa
Hello everyone,
I would appreciate some advice on my simulation.
The System is a Protein attached to a small Funcionalized Surface
composed of ~250 positive carboxyl groups. The hole system is about
220,000 atoms. (amber,tip3p)
The big concern is how to deal with a net charge of almost "-250" ?
(
Hello everyone,
I would like to measure the dihedral energy of certain portions of the same
molecule over the course of a previously calculated trajectory. It's important
that I get the energy of ONLY these portions. I thought of saving the
trajectory of the portion in interest using trjconv. Then
Arindam,
I am tempted to respond by asking how to convert my data into a paper
so I can send it out for publication, but maybe I'll refrain.
Before you can make your xvg file into a graphic, you probably have to
make a plot of the data in the file. Since xvg files are readable by
xmgrace, you mi
Hi Arindam
To read *.xvg files you need the xmgrace software, which is distributed free of
charge, sometimes as a rpm depending on your linux version. It is also
available for Cygwin, but I have never managed to make it work.
Once you have opened the *.xvg file in xmgrace (xmgrace *.xvg), you
David Mobley wrote:
All,
This went out to the revision list and I wanted to follow up on it, so
I figured this is the place to do it.
On 8/17/06, David van der Spoel <[EMAIL PROTECTED]> wrote:
Fixed bug where the long range forces where discarded during energy
minization, normal mode analysis
Hi gmx-users,i have a energy.xvg file, but i am not able to convert it to a jpeg, pdf or png format. in fact any cross platform format so that i can print out or send it for publications. any help in this regard is welcomed. thanks.
arindam
___
gmx-users
All,
This went out to the revision list and I wanted to follow up on it, so
I figured this is the place to do it.
On 8/17/06, David van der Spoel <[EMAIL PROTECTED]> wrote:
Fixed bug where the long range forces where discarded during energy
minization, normal mode analysis and TPI.
What branc
If I am not wrong, what you want to do is to build a topological file correctly
for a cyclic peptide.
You can do this:
For example, your peptide has 5 (n=5) aa: CAAAD,
You can build easily a linear topology file for a six (n+1) aa peptide chain (
with -ter switch answered by none): CAAADC, the l
David van der Spoel wrote:
Yang Ye wrote:
David van der Spoel wrote:
Mark Abraham wrote:
Jerome Henin wrote:
Hi all,
As quite a few people have done before, I am about to try and
convert a CHARMM topology into a GROMACS one. To that effect, I
will probably need one or several programs that
Jerome Henin wrote:
On Wednesday 16 August 2006 23:43, Mark Abraham wrote:
Jerome Henin wrote:
Hi all,
As quite a few people have done before, I am about to try and convert a
CHARMM topology into a GROMACS one. To that effect, I will probably need
one or several programs that will do part of t
Efi Mantzourani wrote:
Hi David,
had a look for the specbond entry, but apparently it is for creating a
bond between ligand and receptor. I don't have that. Mine is not a
special bond. it is just that pdb2gmx tries to find a terminus for all
the chains.
just try it anyway. you may have to s
On Wednesday 16 August 2006 23:43, Mark Abraham wrote:
> Jerome Henin wrote:
> > Hi all,
> >
> > As quite a few people have done before, I am about to try and convert a
> > CHARMM topology into a GROMACS one. To that effect, I will probably need
> > one or several programs that will do part of the
Hi David,had a look for the specbond entry, but apparently it is for creating a bond between ligand and receptor. I don't have that. Mine is not a special bond. it is just that pdb2gmx tries to find a terminus for all the chains. David van der Spoel <[EMAIL PROTECTED]> έγραψε: Efi Mantzoura
[EMAIL PROTECTED] wrote:
Dear users,
What are parameters which differs in invacuo and water simulation apart
from that water is not added in invacuo. I mean what are the things we
have to be considered or not considered while performing invacuo simulation.
regards
you can in principle run wi
Yang Ye wrote:
David van der Spoel wrote:
Mark Abraham wrote:
Jerome Henin wrote:
Hi all,
As quite a few people have done before, I am about to try and
convert a CHARMM topology into a GROMACS one. To that effect, I will
probably need one or several programs that will do part of the job.
W
Joern Lenz wrote:
On Wednesday 16 August 2006 16:32, you wrote:
dear gromacs users,
i am new to gromacs (using version 3.3.1) and trying to simulate an enzyme
which is covalently bound to a piece of dna i.e. a tyrosine is connected to
the dna backbone establishing a phosphodiester group.
but eac
Efi Mantzourani wrote:
Hi all,
I am trying to run a gromacs trajectory on a ligand-receptor complex,
where the ligand is a head-to-tail cyclic peptide. I add the -ter option
in the pdb2gmx command, so that i can turn off the charged termini in
the peptide. Unfortunately, it will only work kee
Hi all,I am trying to run a gromacs trajectory on a ligand-receptor complex, where the ligand is a head-to-tail cyclic peptide. I add the -ter option in the pdb2gmx command, so that i can turn off the charged termini in the peptide. Unfortunately, it will only work keeping the N terminus as
On Wednesday 16 August 2006 16:32, you wrote:
> dear gromacs users,
> i am new to gromacs (using version 3.3.1) and trying to simulate an enzyme
> which is covalently bound to a piece of dna i.e. a tyrosine is connected to
> the dna backbone establishing a phosphodiester group.
> but each time i tr
Dear users,
What are parameters which differs in invacuo and water simulation apart
from that water is not added in invacuo. I mean what are the things we
have to be considered or not considered while performing invacuo simulation.
regards
Anwar
--
Mohd Anwaruddin
Project Ass
David van der Spoel wrote:
Mark Abraham wrote:
Jerome Henin wrote:
Hi all,
As quite a few people have done before, I am about to try and
convert a CHARMM topology into a GROMACS one. To that effect, I will
probably need one or several programs that will do part of the job.
When these are do
Navratna Vajpai wrote:
Dear Prof. David
Thanks for the suggestion. I just had a look for the various force field
options. before starting my simulation I have a little queries..
1) Can I not use the same GROMOS force field g43b1 and then add HA
afterwards by any other software or any other prog
Dear Prof. DavidThanks for the suggestion. I just had a look for the various force field options. before starting my simulation I have a little queries..1) Can I not use the same GROMOS force field g43b1 and then add HA afterwards by any other software or any other program in your package?2)Can I u
Navratna Vajpai wrote:
Dear Mark
Hello.
The force field I used is g43b1 from GROMOS96. I checked the g43b1.atp
file and fond that the HC is defined there which corresponds to Hydrogen
attached to the Carbon. But somehow in the pdb outcome this is not
there. the output pdb file contains only H
Dear MarkHello.The force field I used is g43b1 from GROMOS96. I checked the g43b1.atp file and fond that the HC is defined there which corresponds to Hydrogen attached to the Carbon. But somehow in the pdb outcome this is not there. the output pdb file contains only H atoms corresponding to HN. Now
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