Hi Fernando,
I've obtained the vectors for the rectangular box in g_energy,
using Box_XX, Box_YY and Box_ZZ options; I didn't use the vectors of the
skewed box.)
You have to use the three vectors from the tricilinic representation
to obtain the correct distance in the periodic system. Check
Hi.
Mg is probably in the force field already. You don't need to run it
through pdb2gmx. Add it manually after generation of the topology for
the protein. #include ions.itp in the topology file and add the
correct name (check ions.itp) under [ molecules ]. Be sure to have all
atoms matching in
Hai Everyone ! I hav a small doubt regarding RMSF . How can we calculate
rmsf for helices and sheets only in a protein (excluding loops )???
Thanks for ur valuable time.
--
With Best Wishes
Venkat Reddy Chirasani
M.Tech Bioinformatics
UNIVERSITY OF HYDERABAD
Venkat Reddy wrote:
Hai Everyone ! I hav a small doubt regarding RMSF . How can we calculate
rmsf for helices and sheets only in a protein (excluding loops )???
By using the tool designed for the task with an index file designed for
the task :-)
g_rmsf -n helices_and_sheets.ndx
Mark
process crashes around 100 steps out of 1000 requested.
On Fri, Apr 10, 2009 at 4:32 PM, Justin A. Lemkul jalem...@vt.edu wrote:
nam kim wrote:
I have segmentation fault error while running mdrun_mpi( gromacs 4.0.4).
I have installed gromacs 4.0.4 two month ago and been working fine.
Hi, all,
I am doing shell molecular dynamics and I have read the sw.itp. Now my
question is:
1. For the shell atom, what element should be used in .pdb file, since the
77-78th digits of pdb file is element symbol ?
2. What does the 1 in [ polarization ] part mean in sw.itp?
3. Is it
Shuangxing Dai wrote:
Hi, all,
I am doing shell molecular dynamics and I have read the sw.itp. Now my
question is:
1. For the shell atom, what element should be used in .pdb file, since
the 77-78th digits of pdb file is element symbol ?
Anything you like. Gromacs does not use this
Hi!
I'm am trying to visualize the energy minimization trajectory path of my
protein+ligand in VMD. I imported the .trr file into the ending energy
minimized pdb file, and I was able to see the frames of the trr (53 all
together with nstxout=1). But when I ran the trajectory I saw barely any
nam kim wrote:
process crashes around 100 steps out of 1000 requested.
Fine, but you still haven't answered my question. Do you receive any other
messages?
Do other systems run on the specific hardware you're using? You may just have
some instability in this particular system that is
Halie Shah wrote:
Hi!
I'm am trying to visualize the energy minimization trajectory path of my
protein+ligand in VMD. I imported the .trr file into the ending energy
minimized pdb file, and I was able to see the frames of the trr (53 all
together with nstxout=1). But when I ran the
Hi,
I've installed version 4.0.4 and tried again but still have the same
problem in restarting my simulation with a checkpoint file.
I'm uisng 4 cpus in 1 node and double precision options:
mpirun -np 4 mdrun_d -cpi state.cpt -append yes -cpt 30
The error message is:
Program mdrun_d,
Hello,
I run simulations with polyethylene molecules with harmonic potential for C-H
bonds and Morse potential for C-C bonds. The system consists of 1000 carbon
atoms and 2002 hydrogen atoms. The simulation runs with PBC at constant density
(~0.8 g cm-3) and no pressure coupling. At the
Popov Konstantin wrote:
Hello,
I run simulations with polyethylene molecules with harmonic potential for C-H
bonds and Morse potential for C-C bonds. The system consists of 1000 carbon
atoms and 2002 hydrogen atoms. The simulation runs with PBC at constant density
(~0.8 g cm-3) and no
Thank you for help. The harmonic potential between core and shell is
attractive. The charges they have are opposite, this means that there will
only be attractive force between them. My result also show that they nearly
overlap. Is this reasonable and shell model correctly used? If not, where
Shuangxing Dai wrote:
Thank you for help. The harmonic potential between core and shell is
attractive. The charges they have are opposite, this means that there
will only be attractive force between them. My result also show that
they nearly overlap. Is this reasonable and shell model
I don't know the conditions you use with your system, but sometimes there are
problems when you use pressure coupling in a system with positionally
restrained or fixed atoms.
Cheers.
Lucio.
From: Joe Joe
Sent: Friday, April 10, 2009 12:12 PM
To: Discussion list for GROMACS users
Hi all:
I have a basic question here. I want to simulate a infinite alpha-helix
protein, say alanine represented using a unit cell containning 11 residues.
Now I want to simulate it in GROMACS but don't know how to generate TOP for the
structure, i.e. the connectivity between the 1st residue and
Zhiping Xu wrote:
Hi all:
I have a basic question here. I want to simulate a infinite alpha-helix
protein, say alanine represented using a unit cell containning 11 residues.
Now I want to simulate it in GROMACS but don't know how to generate TOP
for the structure, i.e. the connectivity
I think the local pressure can only be calculated with a modified unsupported
version of gromacs that you can download. However, this was only done with
gromacs version 3.0 not even 3.3
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Hi Gromacs users,
In my simulation, I need to restrain distances between atoms on two protein
molecules. But the Gromacs manual on NOE seems to imply that the atom
indices belong to the same molecule type.
So I am wondering whether it is possible to create distance restraint
between two molecule
Dear Justin
I am doing inflategro process for scaling and
packing of lipid around my protein . the first step is successfully
completed ,there is 9 lipid removed a/c to that I have updated my topology
file ---
; Include forcefield parameters
#include ffG53a6_lipid.itp
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