With xyz periodic boundary conditions, the ions will eventually appear as if
they are diffusing into the extracellular compartment from above as they
diffuse down the -Z and leave the original box, anyway. So unless you actually
need them *only interacting* with the intracellular side by using
Dear James,
I was working for a longer time on ion placement within more or less
equilibrated structures. I found my nearly magical miracle solving those
problems in not using any gromacs tool for producing the input structure
but rather use the free software Packmol:
Mark,
I'm using exact all parameters wich I found in different experimental work.
By the way reducing of integration step to 1fs provide me with better
equilibration of the Ccl4 system ( I've being obtained stabile system
during 3 ns)
but I had a problems during ntp equilibration when I
Dear All
How does the terminal group capping/ionization state will influence the
Free energy obtained from g_wham in umbrella sampling simulation.
Shahid Nayeem
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Hi all!
I'm trying to create a topology file from the pdb using the pdb2gmx
command of gromacs 3.3.1 but I'm encountering some issues. I should
use the flag -tar in order to select interactively the termini, but
with the old version of gromacs this is not implemented and I cannot
use a new one
francesca vitalini wrote:
Hi all!
I'm trying to create a topology file from the pdb using the pdb2gmx
command of gromacs 3.3.1 but I'm encountering some issues. I should
use the flag -tar in order to select interactively the termini, but
with the old version of gromacs this is not implemented
Do you mean that I can just use the new version of pdb2gmx than change
the included forcefield and in case the name of the atoms and it
should work?
2012/2/16 Justin A. Lemkul jalem...@vt.edu:
francesca vitalini wrote:
Hi all!
I'm trying to create a topology file from the pdb using the
francesca vitalini wrote:
Do you mean that I can just use the new version of pdb2gmx than change
the included forcefield and in case the name of the atoms and it
should work?
You still have to fix the incorrect atom name(s), regardless of version. You
can use a new version to make use of
Hi MPID,
I just stepped over your message quite late, so sorry for the late reply.
You can simply generate a new set of tpr files with pull_dim= N N Y, and
use that one in g_wham. g_wham only picks the force constants and
umbrella centers from the tpr files, so you are fine with that.
Hi,
since there is no pull type for curved pathways, you have to generate
the gmx3-type pdo files from your simlation output and use these in
g_wham (g_wham -ip). See g_wham -h for a example header of a pdo file.
Cheers,
Jochen
Am 2/14/12 5:53 PM, schrieb HAO JIANG:
Dear all,
I would
Dear gmx users,
I am calculating the free energy of solvating a small ligand by water, using
FEP method. The free energy is separated into the contribution of electric+vdw.
I find problem for the vdw part.
I am using gromacs-3.3.1. In the top file, I set the state B of ligand where LJ
Hello dear users,
I'm familiar with solvated protein simulations for quite a while now. Recently
I'm beginning to study some membrane systems.
I have created a POPC membrane and now I need to make a proper box. Using
editconf, the box is always larger than the membrane's x and y coordinates,
ACE and NH2 caps are present in the gromacs-4.5.5 distribution for CHARMM27;
To make others, you can compare the existing GMX/charmm27 topology to
the original CHARMM topology files and proceed by analogy (+read manuals!)
Krzysztof
On 2/16/12 5:03 AM, Vasileios Tatsis wrote:
Dear Gromacs
Hi Ricardo,
If you've generated your membrane without taking PBC into account,
then I'd say measuring the extent and setting the box manually
(editconf -box) is the best option you have.
Cheers,
Tsjerk
On Thu, Feb 16, 2012 at 5:44 PM, Ricardo O. S. Soares
ross_...@yahoo.com.br wrote:
Hello
Hello Tsjerk,
Thanks for your reply!
I have take into account PBC for this system. In this case what procedure do I
have to add it in the making of the membrane?
Is the best way to do it with one POPC residue and then multiplying into a
bilayer with genconf or to download a membrane.pdb and
Hi all!
I'm having some issues with the reverse transformation, so I decided
to start from a toy system, alias the 1UBQ present in the martini
tutorial. After running the ./martinize script., before any energy
minimization, I try to reverse the transformation and I encounter the
following error
Hi Francesca,
Can you post your complete workflow?
Cheers,
Tsjerk
On Feb 16, 2012 7:04 PM, francesca vitalini
francesca.vitalin...@gmail.com wrote:
Hi all!
I'm having some issues with the reverse transformation, so I decided
to start from a toy system, alias the 1UBQ present in the martini
So my problem still is
1) During npt without peptide my Ccl4 system expan rapidly in X-dimension.
That produce error on 2nd ns of equilibration
One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the cut-off.
2) During npt
On 17/02/2012 4:46 PM, James Starlight wrote:
So my problem still is
1) During npt without peptide my Ccl4 system expan rapidly in
X-dimension. That produce error on 2nd ns of equilibration
One of the box vectors has become shorter than twice the cut-off
length or box_yy-|box_zy| or box_zz
Mark,
The pure Ccl4 cube was expanded in X dimension during npt phase. By the way
I've been able to prevent it by increasing the ref_p of X up to 5 ussing
semiisotropic pcoupltype
By when I've inserted peptide on the npt of that system my Ccl4 box was
expanded on Z rapidly.
Might this way
On 17/02/2012 5:33 PM, James Starlight wrote:
Mark,
The pure Ccl4 cube was expanded in X dimension during npt phase.
So assuming you simulated long enough to have reasonable convergence,
your model is not stable at the initial volume with whatever that
reference pressure was.
By the
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