Hi,
I modified the changes to the source code as suggested by Dr. Hess and
recompiled Gromacs. The grompp output appears to have advanced by one
line (output below), however the process still terminates with a
segmentation fault. Additional suggestions or ideas for diagnostics
would be appr
Thank you Berk!
Actually I need to freeze two proteins so I have to exclude interactions. I
already tried to use PME and energygrps_excl together, but grompp used to give
me this warning:
Can not exclude the lattice Coulomb energy between energy groups
which is related to PME (I think it i
I just checked similar simulations of mine and Berk's suggestion
accounts for similar discrepancies that I notice on a quick evaluation
where g_traj and g_dist fail to give me the same distance as I obtain
from the pull pos.xvg file. As Berk suggests, once I first trjconv
-center -pbc mol -ur c
Hi,
The exclusions in the topology introduce long range interactions
that require large domain decomposition cells.
The md.log of 4.0.3 will tell you this.
Remove all those exclusions and add energygrp exclusions in the mdp file.
(Or do not use exclusions at all)
Berk
Date: Thu, 22 Jan 2009 12:
Hi,
There could be a problem with periodic boundary conditions.
Do you have multiple molecules in a pull group, or broken molecules?
In that case the COM position of 3.3.3 and g_traj are both incorrect.
The pull code in 4.0 grompp and mdrun are (as far as I know) always correct.
Berk
> Date: Th
Hi everyone;
I am trying to do some simulation using frozen groups on an 8 core computer. I
have tow boxes:
1) Box 1 has two proteins and both of them are kept frozen (I used [exclusions]
directive in topology file to exclude the interactions in each frozen group,
NVT).
2) Box 2 has those t
make_ndx -f my.gro << EOF
r ALA VAL TRP ...
q
EOF
-- original message --
Hello guys,
neone have idea how to mark which are the hydrophobic residue to
supply with make index command and have to calculate the gyration curve.
regards,
___
gmx-users m
Greetings Gromacs users - This note is to announce a new upload in the "user
contributions" section on the Gromacs website. Here is the description:
GIMLi-1.0:
GROMACS Including Monte Carlo Mutation Moves for Mixtures of Lipids
(not official GROMACS!)
The purpose of this modified version of Gro
Hi Jacob,
Check the output from pdb2gmx.
It works with the tutorial files, so the problem is with your input,
not with the program.
Tsjerk
On Thu, Jan 22, 2009 at 5:39 PM, wrote:
> I'm having issues with the pdb2gmx command in gromacs. It does not seem to be
> creating the .gro file for some r
Dear all,
I have encountered an odd behavior with use of the "pull_geometry =
distance" option of the pull code, upon transitioning from Gromacs
version 3.3.3 to version 4.0.3. It appears to be related to the center
of mass distances of the two pull groups, which has an effect of
abruptly di
I'm having issues with the pdb2gmx command in gromacs. It does not seem to be
creating the .gro file for some reason. When I enter the command:
pdb2gmx -f trial1.pdb -p trial1.top -o trial1.gro
I only end with a trial1.top file but no trial1.gro file. However, the pdb2gmx
command appears to work
dota wrote:
Hi.I have recently installed Gromacs-3.3.3. & I want to study protein
folding on a small protein.Where should I get more information about
protein folding in Gromacs, what has been done up until now & how was it
done(except the manual)? I tried but I didn’t find a lot.What kind of
Hi.I have recently installed Gromacs-3.3.3. & I want to study protein folding
on a small protein.Where should I get more information about protein folding in
Gromacs, what has been done up until now & how was it done(except the manual)?
I tried but I didn't find a lot.What kind of force field it
Dear Caty,
You have to make an index file containing groups for each type of atom in one
of your tails (e.g. the sn1-chain), that means for dppc you end up with 15
groups: C11, C12, C13, ...
Each group will have 100 elements.
For the sn2-chain you need to make a separate index file.
Andreas
>
Hi Lin,
Have you tried searching some articles on the matter? You're 10+
postings to this list on the subject haven't yielded much to date. If
you want a better answer, you'll have to be more specific in what type
of data you want to reproduce. Key thing is to understand what you get
from scatteri
koukouli...@eie.gr wrote:
Dear all gmx_users,
I want to calculate the order parameter after the incorporation of a
molecule of DHA in the DPPC Bilayer (100 DPPC lipids).
I have read in the manual that the program can gives an idea of the
ordering of a molecule from head to tail and I have
Dear all gmx_users,
I want to calculate the order parameter after the incorporation of a molecule
of DHA in the DPPC Bilayer (100 DPPC lipids).
I have read in the manual that the program can gives an idea of the ordering of
a molecule from head to tail and I have read that I have to construct a
What do you want to do? Please take some time to phrase a proper question.
Tsjerk
On Thu, Jan 22, 2009 at 7:04 AM, ravi sharma wrote:
>
> Hello guys,
> neone have idea how to mark which are the hydrophobic residue to supply with
> make index command and have to calculate the gyration curve.
>
>
Hi,
It seems that I have only tested the cylinder option after the very first
implementation
of the domain decomposition.
There are two obvious bugs:
On line 967 of src/mdlib/pull.c ind_loc should be snew'ed instead of ind.
On line 170 of src/mdlib/pullutil.c the loop should go to 1+pull->ngrp,
On Jan 22, 2009, at 6:38 AM, li jianguo wrote:
Dear all,
I am running MD simulaiton using Gromacs for alpha-helilx
polyalanine solution. The initial configuraiton of polyalanine
peptide was generated using Discovery Studio. I follow the procedure
below:
1: solvate the polyalanine in a w
I have no experience with polyalanine, but you may try position restraint MD
for longer (500 ps) and energy minimisation of the the whole system afterwards.
Andreas
>
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of li jianguo
Sent: 22 January
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