Hi ALL,
I tried to calculate the helix tilt of a single helix (TM5) among 7 helices
using g_bundle. In the index file I defined the two groups (top bottom) as
the C-alpha of the first 5 and last 5 residues of TM5 respectively. But in
the bun_tilt.xvg file I am getting the values as:
Dear All
I did 10ns simulation of three peptide residue solvated in water. Each
peptide residue is 26 residue long. In final .gro file it is showing total
78 residue which is O.K. as 3x26=78. For inserting three similar peptide I
used genconf command. when I run dssp I get total residue as 80. The
- Original Message -
From: sonali dhindwal sonali11dhind...@yahoo.co.in
Date: Monday, May 24, 2010 14:32
Subject: [gmx-users] simulation crashed because of LINCS error
To: Discussion list for GROMACS users gmx-users@gromacs.org
---
|
Dear Justin, Thanks alot for the feedback, I forgot to set the Clj and the Cqq
and the ligand options for g_lie, I set them and I got the energy calculated
and it is reasonable value. I am waiting to do the same thing for the whole
complex (protein, ligand and sol) and get an estimate of the
Thanks Mark for the reply,
I think I have mistakenly written 30 instead of 300 for ref_t in temp coupling,
So if that could be the problem ?
because I have equilbrated the protein before simulation but time is for 20
ps. Is that very short time period?
Acually I want to stress here that i have
Have you tried using the -z option to calculate the angle with respect
to to the z axis? I vaguely remember having an issue like this a few
years ago and this fixed the problem, sorry I can't be more specific.
Cheers
Tom
Anirban Ghosh wrote:
Hi ALL,
I tried to calculate the helix tilt of
Dear Luca, dear all,
thank you for your hints. I made some trials with my systems and these are
my answers to your questions:
- my system is a protein (with or w/o ligand) in solvent (water SPC).
Following your suggestions, I tried to perform an EM on the protein w/o
ligand after the editconf
sonali dhindwal wrote:
Thanks Mark for the reply,
I think I have mistakenly written 30 instead of 300 for ref_t in temp
coupling,
So if that could be the problem ?
because I have equilbrated the protein before simulation but time is
for 20 ps. Is that very short time period?
Acually I
shahid nayeem wrote:
Dear All
I did 10ns simulation of three peptide residue solvated in water. Each
peptide residue is 26 residue long. In final .gro file it is showing
total 78 residue which is O.K. as 3x26=78. For inserting three similar
peptide I used genconf command. when I run dssp I
Hassan Shallal wrote:
Dear Justin, Thanks alot for the feedback, I forgot to set the Clj and the
Cqq and the ligand options for g_lie, I set them and I got the energy
calculated and it is reasonable value. I am waiting to do the same thing for
the whole complex (protein, ligand and sol) and
Anna Marabotti wrote:
Dear Luca, dear all,
thank you for your hints. I made some trials with my systems and these are
my answers to your questions:
- my system is a protein (with or w/o ligand) in solvent (water SPC).
Following your suggestions, I tried to perform an EM on the protein w/o
tekle...@ualberta.ca wrote:
Dear Gromacs Users,
I run an MD simulation of a pure solvent and found out that the density
of the solvent deviated a little bit from the actual experimental data.
MD density is 880g/ml and the experimental data is 866g/ml. Is this
reasonable for toluene
- my system is a protein (with or w/o ligand) in solvent (water SPC).
Following your suggestions, I tried to perform an EM on the protein w/o
ligand after the editconf step (i.e. I created the topology with
pdb2gmx,
created a cubic box with editconf, then I used grompp+mdrun to
perform EM).
I
Another way to try to understand what is going on wrong is to cut away
the residue 1 (atom 1)
and see what happens: in this case you will understand if the guilty
is the residue 1 (as LINCS seems, at least, to suggest) or anything else
in the protein.
Cheers
Luca
Dear Luca, dear all,
Dear Justin, dear Luca,
here's the answer to your questions:
- I'm currently using the classical forcefield gromos96 43a1 (choice 0
in pdb2gmx). After producing the topology, the only warning I see from
pdb2gmx is this one: WARNING: there were 0 atoms with zero occupancy and 63
atoms with
Anna Marabotti wrote:
Dear Justin, dear Luca,
here's the answer to your questions:
- I'm currently using the classical forcefield gromos96 43a1 (choice 0
in pdb2gmx). After producing the topology, the only warning I see from
pdb2gmx is this one: WARNING: there were 0 atoms with zero occupancy
Hi Justin
I choose group 5 main chain for dssp calculation
Shahid Nayeem
On 5/24/10, Justin A. Lemkul jalem...@vt.edu wrote:
shahid nayeem wrote:
Dear All
I did 10ns simulation of three peptide residue solvated in water. Each
peptide residue is 26 residue long. In final .gro file it is
shahid nayeem wrote:
Hi Justin
I choose group 5 main chain for dssp calculation
Do you have any capping groups (N-acetyl, C-amine, etc)?
-Justin
Shahid Nayeem
On 5/24/10, *Justin A. Lemkul* jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
shahid nayeem wrote:
Dear All
Hi
No i dont have any capping group
shahid Nayeem
On 5/24/10, Justin A. Lemkul jalem...@vt.edu wrote:
shahid nayeem wrote:
Hi Justin
I choose group 5 main chain for dssp calculation
Do you have any capping groups (N-acetyl, C-amine, etc)?
-Justin
Shahid Nayeem
On 5/24/10,
Hi There,
I want to use a large simulation box. I did a trial with 15 * 15 * 15 nm box
for 100 steps. genbox_d generates 110k water molecules, or 330k atoms.
It looks like that gromacs can run that large number of atoms. I am sure it
will take a long long long time. However if I really want to
shahid nayeem wrote:
Hi
No i dont have any capping group
Then I have no idea what's going on. The only data that present a problem are
in the very first frame, indicating that the HEBT+coil content totals 80
residues. All the other frames look fine. It could be that the algorithm is
- Original Message -
From: Yan Gao y1...@ucsd.edu
Date: Tuesday, May 25, 2010 3:02
Subject: [gmx-users] large sim box
To: Discussion list for GROMACS users gmx-users@gromacs.org
Hi There,
I want to use a large simulation box. I did a trial
with 15 * 15 * 15 nm box for 100 steps.
Hi, everyone,
Recently our school upgraded the clusters for us. And they install the
Gromacs-4.0.7 for us. Before I always used Gromacs-4.0.3, the scripts used
for parallel running works well.
My script is as follows:
#PBS -l nodes=4:ppn=2
#PBS -N pr-impd1-wt
#PBS -j oe
module load gromacs
Yi Peng wrote:
Hi, everyone,
Recently our school upgraded the clusters for us. And they install the
Gromacs-4.0.7 for us. Before I always used Gromacs-4.0.3, the scripts
used for parallel running works well.
My script is as follows:
#PBS -l nodes=4:ppn=2
#PBS -N pr-impd1-wt
#PBS -j oe
I modified the .mdp file, created a full system tpr, then ran it
through tpbconv, then ran mdrun using the original xtc. It says the
atom numbers don't match.
mdrun -rerun md.xtc -v -s lig.tpr
---
Program mdrun, VERSION 4.0.5
Source code file:
John Shultz wrote:
I modified the .mdp file, created a full system tpr, then ran it
through tpbconv, then ran mdrun using the original xtc. It says the
atom numbers don't match.
mdrun -rerun md.xtc -v -s lig.tpr
---
Program mdrun, VERSION
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