Hi Arneh,
I think you're out of luck here. However, this is an excellent
exercise to get started with writing custom made analysis tools :)
Alternatively, you could output the coordinates for the C and O using
g_traj and use a script to calculate the angles with the z-axis, in
case it's a single
Hi Fernando,
Did you try using version 3.2 yourself?
Tsjerk
On 7/14/07, zazeri <[EMAIL PROTECTED]> wrote:
Hi to all! :D
I'm facing a problem with the xtc file. It has been
getting me the following error:
Program trjconv, VERSION 3.3.1
Source code file: xtcio.c, line: 83
Fatal error:
Magic N
Hi Mark,
From the log it seems you're trying to solvate your protein (-cp
gmx.pdb) with your protein (-cs gmx.gro)! Read the manual on genbox...
Tsjerk
On 7/16/07, Mark Zottola <[EMAIL PROTECTED]> wrote:
I am trying to run genbox and am getting a segmentation fault. After
running pdg2gmx, I
Gurpreet,
my system was going fine at that time but when i used the genion command to
add ions , i found that my protein was broken into parts.
what could be the reason for this ?
PBC?
While running the genion it usually asked for the group into which we want
to add the ions so i have che
Dear gmx-users,
Recently I want to perform MD for protein with implicit solvent model.
Gromacs does not seem to support it.
Could you let me know where to find information about implicit solvent
simulation with Gromacs?
Also I will be glad if you tell me your opinion about the implicit solvent
si
Hello!
Could you please help me to understand solution as well? I just plotted these
functions so that I combined sigma and epsilon values using rule 3
sigma(ij)=(sigma(i)*sigma(j))^(1/2)
epsilon(ij)=(epsilon(i)*epsilon(j))^(1/2)
and corresponding C6 (4*epsilon*sigma^6) and C12 (4*epsilon*sigma^
Thanks Tsjerk for you reply
i did not get your point . i think you are asking me whether i used PBC or
not , so i want to tell you that the .tpr file which i used for genion
command was created without using PBC.
but will it make any difference ?
Thanks
With Regards
Gurpreet
On 7/16/07, Tsjerk W
Gurpreet,
I didn't ask whether you used PBC, I suggested it was due to PBC.
Check the archives for "broken molecules" and such.
Tsjerk
On 7/16/07, gurpreet singh <[EMAIL PROTECTED]> wrote:
Thanks Tsjerk for you reply
i did not get your point . i think you are asking me whether i used PBC or
no
Sorry, I really didn't get, what your goal is and what, in fact, you
really want to do.
For free energy calculations, you can
- either do Thermodynamic integration (the lambda 0/1 stuff)
- or pulling (force probe) and afterwards use Jarzynskis theorem
- or umbrella sampling together with WHAM (i
Hi guys,
My first question is with regards to the size relationship
between rlist and rvdw/rcoulomb, and consequently the
meaning of rlist.
I found an excellent question on this exact same subject
posted couple of years ago, but I couldn't find the answer to
it. I copy parts of the question here
Hi guys,
My first question is with regards to the size relationship
between rlist and rvdw/rcoulomb, and consequently the
meaning of rlist.
I found an excellent question on this exact same subject
posted couple of years ago, but I couldn't find the answer to
it. I copy parts of the question here
Thanks Tsjerk
I referred the mail about the broken molecules but there the problem is i
think somewhat different. in that case broken molecules are coming becasue
of the PBC . since PBC is being used that is why some part of the molecule
is coming from the other side of box and its looking as i
Hi Gromacs crew and others
I have a few questions regarding the equilibration of the system
my system is linear PPG (polyprpylene glycol)polymer chain (melts in vaccum)
with the following details
number of monomers = 22
Total number of atoms = 3664
total number of chains = 16
My chains are aran
From: "Frankie Montenegro" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: gmx-users
Subject: [gmx-users] a) rlist vs rvdw/rcoulomb size confusion,and b)
reduced units
Date: Mon, 16 Jul 2007 06:56:41 -0400
Hi guys,
My first question is with regards to the size relatio
SeungPyo Hong a écrit :
Dear gmx-users,
Recently I want to perform MD for protein with implicit solvent model.
Gromacs does not seem to support it.
Could you let me know where to find information about implicit solvent
simulation with Gromacs?
Also I will be glad if you tell me your opinion abo
Mahnam a écrit :
In God We Trust
Hello Dear Dr David van der Spoel
Thank you for your quick response. I had used constraints before md
simulation.
I have done energy minimization and position restraint (20ps) (with
constraints=all bonds )and then md simulation at 100 K, 200K and 300K for
100
Mahnam a écrit :
In God We Trust
Hello Dear Dr David van der Spoel
Thank you for your quick response. I had used constraints before md
simulation.
I have done energy minimization and position restraint (20ps) (with
constraints=all bonds )and then md simulation at 100 K, 200K and 300K for
100
Hi Ann,
> So my first question is
>
> wether this can be possible or not? or am I doing something wrong?
> if so, then how can i rectify the same error?
I think you should definitely use 'editconf -density' to rescale your
simulation box to the right density. editconf automatically rescales
Jeroen van Bemmelen wrote:
Hi Ann,
So my first question is
wether this can be possible or not? or am I doing something wrong?
if so, then how can i rectify the same error?
I think you should definitely use 'editconf -density' to rescale your
simulation box to the right density. editconf
Dear gmx-users,
does anyone know if there are reasonable parameters for hydorgen
peroxide H2O2 around? I found few references that present parameters for
H2O2 via google, but in none of the cases it was clear to me where the
parameters come from exactly and whether they have been tested proper
Hello,
What I want to do is calculate the free energy difference of pulling the
ligand away from the receptor. I want to do it using theromdynamic
intergration using the Lamda 0/1 stuff. I am just not clear of the
procedure of how to do it.
I want to constraint several distances between the ligan
You should get identical plots. I think rule 1 and rule 3 are equivalent.
On 7/16/07, Janne Hirvi <[EMAIL PROTECTED]> wrote:
Hello!
Could you please help me to understand solution as well? I just plotted
these
functions so that I combined sigma and epsilon values using rule 3
sigma(ij)=(sigma
If i understand correctly then rlist is the short range cutoff inside which
the forces on the atoms are calculated every step (and the neighbour list is
updated every nstlist steps).
If you specify a value of rvdw or rcoulomb larger than rlist then the
forces on the atoms between rlist and rvdw/
Hi, All,
If there are multi-definitions of the same dihedral in topology file, how
will gromacs treat it? Using the second one, or the addition of the two
items?
The reason for my asking this is: a dihedral potential function like the
following needs to be realized ,
V = sum(Cn*cos(phi)^n), n=1
ok, thanks. I like Chris's suggestion. I'll try using matlab to parse
it out (b/c matlab can easily ingest column formatted data),
Arneh
Tsjerk Wassenaar wrote:
Hi Arneh,
I think you're out of luck here. However, this is an excellent
exercise to get started with writing custom made analysis
Hi Arneh,
I'd sort of do the same, but would use R (http://cran.r-project.org/)
:) Just a matter of taste (and of sticking to free, open-source
software).
Tsjerk
On 7/17/07, Arneh Babakhani <[EMAIL PROTECTED]> wrote:
ok, thanks. I like Chris's suggestion. I'll try using matlab to parse
it ou
Hi Gurpreet,
You probably performed energy minimization without a box, without PBC.
Then you generated a box using editconf. That's where the PBC comes
in. With genbox you fill the thing with solvent, and running grompp
then will provide you a run input file, which is set up to be used for
a simu
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