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
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
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
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
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*
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
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
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
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http://lists.gromac
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
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-
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
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
>
> 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
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
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
> 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
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
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
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
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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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
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
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
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
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
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
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
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
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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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
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
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
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 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 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
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