On 12/17/2012 08:06 PM, Justin Lemkul wrote:
It seems to me that the system is simply crashing like any other that
becomes unstable. Does the simulation run at all on plain CPU?
-Justin
Thank you very much Justin, it's really helpful. I've checked that the
structure after minization and
Hi KT,
If you mean concatenating frames in .gro files, you can use trjcat or just
cat. If you mean merging the coordinates, it's a wee bit more complicated.
Since you also ask for top files, I guess that's the case. Here's a snippet
of python code that will do the trick:
#!/usr/bin/env python
18 dec 2012 kl. 09.30 skrev Tsjerk Wassenaar:
Hi KT,
If you mean concatenating frames in .gro files, you can use trjcat or just
cat. If you mean merging the coordinates, it's a wee bit more complicated.
Since you also ask for top files, I guess that's the case. Here's a snippet
of python
there's also an executable topology merger available written in python
called gromacs_topology_merger.py as part of a the software package
ZIBMolPy designed for conformational analysis at
https://github.com/CMD-at-ZIB/ZIBMolPy
given (in the same directory) a topology file topol.top (argument
Dear fatemeh,
in the topology file there is a section called [ bonds ] where the covalent
bonds are listed. You should add you bonds there. But I think modifing
specbonds.dat is easier because it allows pdb2gmx to do the dirty job :)
Anyway, f you have to simulate bond breaking, you can use Morse
thank all so much :-)
KT
On Tue, Dec 18, 2012 at 4:12 PM, Vedat Durmaz dur...@zib.de wrote:
there's also an executable topology merger available written in python
called gromacs_topology_merger.py as part of a the software package
ZIBMolPy designed for conformational analysis at
Sorry, I found the error. There was a bond -C N missing in the rtp file.
Cheers,
Jochen
Am 12/17/12 5:28 PM, schrieb Jochen Hub:
Hi all,
I try to generate a topology using pdb2gmx of a protein that contains a
non-native amino acid, that is lysine with some more atoms, which is
treated a one
On 12/18/12 10:30 AM, Kieu Thu Nguyen wrote:
Dear All,
Are there any difference in nvt.mdp and npt.mdp files between MD-CG and
MD-AA ?
Settings in the .mdp file are dictated by the chosen force field. Every force
field is different and requires proper settings.
-Justin
--
Hi,
I have a general question on cutoff values.
I am using an AMBER03 ff and in a number of papers/tutorials the cutoffs for
vdw/coulomb are reported as low as 0.8 (and up to 1.2 - 1.4 depending on the
interaction type). As far as I understand, increasing this value a bit will
not harm unless
On 12/18/12 1:22 PM, zugunder wrote:
Hi,
I have a general question on cutoff values.
I am using an AMBER03 ff and in a number of papers/tutorials the cutoffs for
vdw/coulomb are reported as low as 0.8 (and up to 1.2 - 1.4 depending on the
interaction type). As far as I understand, increasing
Justin Lemkul wrote
You need a .tpr file and can re-wrap the periodic image with trjconv -pbc
mol -ur compact.
Funny, it needs a file which I don't find:
g_trjconv -f nvt_minimized.trr -o nvt_minimized_compact.xtc -pbc mol -ur
compact
Program g_trjconv, VERSION 4.5.5
Source code file:
On 12/18/12 1:29 PM, Yun Shi wrote:
Hi all,
I understand a suffix of com indicates center of mass, but how about
cog and the prefixes whole and part?
COG = center of geometry.
From g_select -select 'help all' you will find:
3. POSTYPE of ATOM_EXPR calculates the specified positions for
On 12/18/12 1:44 PM, zugunder wrote:
Justin Lemkul wrote
You need a .tpr file and can re-wrap the periodic image with trjconv -pbc
mol -ur compact.
Funny, it needs a file which I don't find:
g_trjconv -f nvt_minimized.trr -o nvt_minimized_compact.xtc -pbc mol -ur
compact
Program
Justin Lemkul wrote
If you don't specify an actual file name to -s, then all Gromacs tools
look for a default file name, which in this case is topol.tpr. Since
you've run a simulation, clearly you have a .tpr file, which is what you
need to provide to -s.
I have only one .tpr file - the
On 12/18/12 2:02 PM, James Starlight wrote:
Dear Gromacs Users!
I'm looking for 150-200 lipid bilayer ( POPC or POPE) parametrized in
charmm27 or charmm36 force field and pre-equilibrated in NPT
conditions. I'll bevery thankfull to anybody who provide me with the
coordinates as well as itp
On 12/18/12 2:04 PM, zugunder wrote:
Justin Lemkul wrote
If you don't specify an actual file name to -s, then all Gromacs tools
look for a default file name, which in this case is topol.tpr. Since
you've run a simulation, clearly you have a .tpr file, which is what you
need to provide to -s.
OK, so there are a lot of necessary dependencies in the command...
Went to read the manual
Thank you.
--
View this message in context:
http://gromacs.5086.n6.nabble.com/Actual-box-size-tp5003850p5003890.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users
On 12/18/12 3:59 PM, XUEMING TANG wrote:
Hi there
I searched through the website for g_sans, which is a simple tool to
compute Small Angle Neutron Scattering spectra. But I cannot find it in
gromacs folder?
I found it in the following website:
Hi Justin
Thank you for this information. I am looking forward for the code to be
ready!
Happy holidays!
Best!
Xueming
On Tue, Dec 18, 2012 at 4:10 PM, Justin Lemkul jalem...@vt.edu wrote:
On 12/18/12 3:59 PM, XUEMING TANG wrote:
Hi there
I searched through the website for g_sans,
Hi,
g_sans is already in the master version of Gromacs (Justin's link is to
g_nse) but it won't be part of 4.6 instead it will be part of 5.0. You can
get this version from git (git clone git://git.gromacs.org/gromacs.git). As
an alternative you could use http://www.sassena.org/ (disclaimer the
Thank Justin !
On Tue, Dec 18, 2012 at 10:31 PM, Justin Lemkul jalem...@vt.edu wrote:
On 12/18/12 10:30 AM, Kieu Thu Nguyen wrote:
Dear All,
Are there any difference in nvt.mdp and npt.mdp files between MD-CG and
MD-AA ?
Settings in the .mdp file are dictated by the chosen force
Dear Prof. Roland:
Thank you very much for the information! I need to do study more on SANS.
If use of your method, would like to cite your work!
Happy holidays and best wishes!
Xueming
On Tue, Dec 18, 2012 at 4:22 PM, Roland Schulz rol...@utk.edu wrote:
Hi,
g_sans is already in the master
Dear Users,
Why I run the command genbox -cp protein_box.gro -ci hfi.gro -nmol
1534 -cs spc216.gro -p control.top -o protein_mixsol.gro.
And the result show like below.:
Grid: 15 x 15 x 11 cells
nri = 9466, nrj = 77062
Try 9579box_margin = 0.45overlap:
Neighborsearching with a cut-off of 0.48
On 12/18/12 9:47 PM, Nur Syafiqah Abdul Ghani wrote:
Dear Users,
Why I run the command genbox -cp protein_box.gro -ci hfi.gro -nmol
1534 -cs spc216.gro -p control.top -o protein_mixsol.gro.
And the result show like below.:
Grid: 15 x 15 x 11 cells
nri = 9466, nrj = 77062
Try 9579box_margin
Justin, thanks again.
As I understood gromacs already had had parameters for charmm lipid so
the main approach is to do ITP file for 1 lipid by means of pdb2gmx
isnt it?
By the way is there any way to convert PSF or CRD file to PDB?
I've found suitable bilayer for my simulation but it lack such
On 2012-12-19 10:16:09AM +0530, Archana Sonawani wrote:
Hi,
I want to simulate a peptide using SDS micelle. The peptide is random
coil,
but I want it to be helical; therefore, I will use TFE for inducing
helix.
You use TFE in a wet lab to physically induce helicity in real life. For
http://cesium.hyperfine.info/~peter/gromacs/popc36/
has a fully gromacs compatible charmm36 238 POPC bilayer with 21524 waters
On 2012-12-18 09:07:22PM -0800, James Starlight wrote:
Justin, thanks again.
As I understood gromacs already had had parameters for charmm lipid so
the main approach
Read through the log file to find out what atoms are causing the system to
crash. I also prefer running mdrun -v and capturing that too, since it
provides similar log data but does not output the energy tables.
You also did not specify what the final maximum forces were in the system
after the
Peter, many thanks!
Could you tell me is there any differences in atom types between
charmm27 and charmm36 ff? I'd like to simulate receptor-ligand complex
in that bilayer where ligand molecule would be parametrized by
Swiss-param ( make topology for the ligands in charmm27 ff). So
because
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