Dear administrators of gmx-users list,
I would like to report a problem in the gmx-users list archive (or at least
in its visualization in the Web site). Starting from 2011, when I search in
the archive on the Gromacs web site, I can see that multiple copies of
identical messages are reported in th
On 19/05/2011 6:25 PM, Anna Marabotti wrote:
Dear administrators of gmx-users list,
I would like to report a problem in the gmx-users list archive (or at
least in its visualization in the Web site). Starting from 2011, when
I search in the archive on the Gromacs web site, I can see that
multip
Dear gmx-users,
I would like to simulate the conformational behaviour of a peptide
covalently anchored to a rigid support with its N- and C-ter. I'm not
interested in simulating the support, so I wonder if there is a way to
simulate the peptide with its N- and C-ter fixed. Could freezegrps work for
On 19/05/2011 7:09 PM, Anna Marabotti wrote:
Dear gmx-users,
I would like to simulate the conformational behaviour of a peptide
covalently anchored to a rigid support with its N- and C-ter. I'm not
interested in simulating the support, so I wonder if there is a way to
simulate the peptide with
Hi ALL,
I am trying to calculate the lateral diffusion coefficient of a protein in a
bilayer (CG simulation using MARTINI FF). The simulation length is 5
micro-seconds. I wanted to know based on what should i set the values of
-beginfit and -endfit and also the value for -trestart. Is it necessary
Anirban Ghosh skrev 2011-05-19 11.58:
Hi ALL,
I am trying to calculate the lateral diffusion coefficient of a
protein in a bilayer (CG simulation using MARTINI FF). The simulation
length is 5 micro-seconds. I wanted to know based on what should i set
the values of -beginfit and -endfit and al
uctuation of the peptide into
> the solvent?
Not sure what you mean.
> Finally, do I have to add special constraints/restraints to my molecule?
Depends on the strategy.
Mark
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vidhya sankar wrote:
Thank you Dr Justinj,
To do SMD should i create centre of mass
of my reference (protein) and pull group (ligand)? if i need to create ,
which tool of gromacs generate to be used .?
How to include this center of mass in SMD .mdp files
N
Dear gromacs users,
1. I have got 3 MD-outputs for the same protein (3 runnings for 100 ns).
I want to make a distance matrix (*g_mdmat*) for the average trajectory of
these 3 runnings.
*g_mdmat* gives an average matrix for one trajectory, but I want to get it
for the average trajectory.
I tried t
Hi ALL,
I have a long simulation trajectory of 3 micro-seconds of multiple protein
monomers in a lipid bilayer.
Which -pbc option should be used with trjconv to process the trajectory
before carrying out any analysis? I am using -pbc nojump, is it correct? Or
should I use -pbc whole?
Thanks a lot
Anirban Ghosh wrote:
Hi ALL,
I have a long simulation trajectory of 3 micro-seconds of multiple
protein monomers in a lipid bilayer.
Which -pbc option should be used with trjconv to process the trajectory
before carrying out any analysis? I am using -pbc nojump, is it correct?
Or should I u
Yulian Gavrilov wrote:
Dear gromacs users,
1. I have got 3 MD-outputs for the same protein (3 runnings for 100 ns).
I want to make a distance matrix (*g_mdmat*) for the average trajectory
of these 3 runnings.
*g_mdmat* gives an average matrix for one trajectory, but I want to get
it for
Justin A. Lemkul skrev 2011-05-19 14.30:
Yulian Gavrilov wrote:
Dear gromacs users,
1. I have got 3 MD-outputs for the same protein (3 runnings for 100 ns).
I want to make a distance matrix (*g_mdmat*) for the average
trajectory of these 3 runnings. *g_mdmat* gives an average matrix
for
Please do not send unsolicited email requesting private help. I am
forwarding this to the appropriate forum.
On point, I think the examples and explanations given in various manual
sections deal with your case.
Mark
Original Message
Subject:energy groups in tabulate
Hey,
If you can sum them, the only thing needed afterwards is updating the
color labels. Like per awk (dividing by two):
awk -F\" '/#/{$4=$4/2}1' file.xpm
Cheers,
Tsjerk
On Thu, May 19, 2011 at 2:43 PM, Erik Marklund wrote:
> Justin A. Lemkul skrev 2011-05-19 14.30:
>>
>>
>> Yulian Gavrilov
tide into
the solvent?
Not sure what you mean.
Finally, do I have to add special constraints/restraints to my molecule?
Depends on the strategy.
Mark
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Hi,
I have started a lengthy equilibration run, and I just realized that I have
one of my parameters set incorrectly in my mdp file. Is there any way that
I can manually abort the run?
I am using Gromacs 4.5.4 with parallel simulation with MPI and the command:
mpirun -machinefile cp -np 8 md
Andrew DeYoung wrote:
Hi,
I have started a lengthy equilibration run, and I just realized that I have
one of my parameters set incorrectly in my mdp file. Is there any way that
I can manually abort the run?
I am using Gromacs 4.5.4 with parallel simulation with MPI and the command:
mpiru
Hello,
I am trying a simulation for water dimer in vaccum (gas phase).
Here I run the simulation with following steps
This is the .pdb file before energy minimization
TITLE S C A M O R G
REMARKTHIS IS A SIMULATION BOX
CRYST13.0003.0003.000 90.00 90.00 90.00 P 1
> the equlibration file I used
>
> title = cpeptid position restraining
> cpp = /usr/bin/cpp
> constraints = none
> integrator = md
> dt = 0.001 ; ps !
> nsteps = 100 ; total 1.0 ps.
> nstcomm
if I set pbc=xyz in energy minimization mdp file then I get following error
ERROR: can only have neighborlist cut-off zero (=infinite)
with coulombtype = Cut-off or coulombtype = User and simple neighborsearch
without periodic boundary conditions (pbc = no) and
rcoulomb and rvdw set to zero
ERRO
Vitaly Chaban wrote:
the equlibration file I used
title = cpeptid position restraining
cpp = /usr/bin/cpp
constraints = none
integrator = md
dt = 0.001; ps !
nsteps = 100 ; total 1.0 ps.
nstcomm
>
> For vacuum systems, "pbc = no" in conjunction with zero cutoffs is correct
> to obtain a gas-phase system.
For reasonably large box, this is the same heck.
Nilesh: visualize your system, using VMD or ngmx. The behavior of your
molecular cluster during the first ps will provide an answer. Are
Very good.
Have you take a moment to define the box in the GRO file?
--
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
On Thu, May 19, 2011 at 4:05 PM, Nilesh Dhumal wrote:
> if I set pbc=xyz in energy minimization mdp file then I get
Vitaly Chaban wrote:
For vacuum systems, "pbc = no" in conjunction with zero cutoffs is correct
to obtain a gas-phase system.
For reasonably large box, this is the same heck.
Setting a box size and using "pbc = xyz" precludes the use of infinite cutoffs,
which should be the most rigorous
I am getting ab error with the newest version of the martini model in which
seq2itp, atom2cg generate structures with a topology mismatch if there are
any alanines in the structure 9. mutating out the alanines seems to resolve
the problem? are there any bug fixes out there?
thanks
jeremy
--
gmx-
jeremy adler wrote:
I am getting ab error with the newest version of the martini model in
which seq2itp, atom2cg generate structures with a topology mismatch if
there are any alanines in the structure 9. mutating out the alanines
seems to resolve the problem? are there any bug fixes out there
Hi,
I have a question about using X-ray PDB files for simulations:
1. Is there any rule of thumb on how good a resolution is required for
simulations?
I know it has nothing to do with GROMACS.
Thanks for your insight.
Simon
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromac
On 20/05/2011 3:45 AM, Justin A. Lemkul wrote:
Andrew DeYoung wrote:
Hi,
I have started a lengthy equilibration run, and I just realized that
I have
one of my parameters set incorrectly in my mdp file. Is there any
way that
I can manually abort the run?
I am using Gromacs 4.5.4 with parall
On 20/05/2011 7:38 AM, simon sham wrote:
Hi,
I have a question about using X-ray PDB files for simulations:
1. Is there any rule of thumb on how good a resolution is required for
simulations?
Not really. The lower the resolution, the more likely that the initial
conditions for the simulatio
Dear Gmx users,
I am trying to do minimization of my system .i
have no problem wehen i grompp it but when i do the mdrun its giving me
some segmentation error.I had attached the output of grompp and mdrun
below.Any suggestions please.Thanks in advance
*OUTPUT OF GROMPP*
sreelakshmi ramesh wrote:
Dear Gmx users,
I am trying to do minimization of my system
.i have no problem wehen i grompp it but when i do the mdrun its giving
me some segmentation error.I had attached the output of grompp and
mdrun below.Any suggestions please.Tha
hai,
to check if my table is correct i just copied the 6-9 table
for /share/top to local directory ( to check if the prob is same with any
other potential) and grompped it and when i did the mdrun i am still getting
the same error.Any suggestions.
On Fri, May 20, 2011 at 6:29 AM, Jus
1. you're not doing energy minimization as your title suggests, please
use a better title:
integrator = md
2. generally, when you have a problem it is useful to try to simplify
the system (e.g. get rid of those tables) and try to reproduce the
problem with the simplest system possible be
dear gmx-users,
During equilibriation i get the following error.Any
suggestions please.
*grompp*
WARNING 1 [file npt.mdp]:
The sum of the two largest charge group radii (2.369582) is larger than
rlist (1.00)
This run will generate roughly 73 Mb of data
There wa
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