Hi,
if there is a protein in your system you should have protein as standard group.
Maybe you use a template mdp file in which the temperature coupling group is
protein. if you have no protein in your simulation check the mdp files for
tc-grps and adjust accordingly.
Max
On Jun 3, 2015,
Hello,
In your command line you do not specify an index file. Maybe you need to
generate one. Check out usage of make_ndx.
Hope this helps
Victor
2015-06-03 13:41 GMT-05:00 marzieh dehghan dehghanmarz...@gmail.com:
Hi every body
I create a covalent bond and now I want to held MD by
Dear Tsjerk,
Yes, you are right. I want to fix the COM of the reference group (one end of a
triple helix), and pull the other end. I tried to freeze the reference group,
but found this setting restricted the unfolding process of my triple helix.
That's why I want to find a way to fix the COM
i want to simulate a system having membrane and proteins with pbc=no to
allow surface effects. I use the following settings in my production mdp
file :
Run parameters
integrator = md; leap-frog integrator
nsteps = 1 ; 2 * 1 = 2 ms
dt =
On 6/3/15 3:46 AM, Lovika Moudgil wrote:
Hi...thanks for reply Peter and Mark I tried with temperature coupling
. But things are still same ...
Hi ... Mark would you like to explain this factor to me ??
Using a plain cutoff in the condensed phase is outdated methodology that is very
On 6/3/15 12:00 AM, Kevin C Chan wrote:
Thanks Justin,
I have long been confused by atom names and types in Gromacs topology. I
have just went through the manual again, and it confirms me that what we
read directly in ffbonded.itp under GMXHOME/share/gromacs/top/oplsaa.ff are
atomtypes. In
Hi, I'm not accustomed with coarse grained, but from the little stuff I know on
MD in order to keep a box's size constant you have to use an NVT simulation not
an NPT. Meaning don't keep pressure constant but rather the volume. Do double
check though, I might be wrong.
Hi Tsjerk,
So what different between nstcomm nsteps case and comm-mode = none case?
Because when I set this option (comm-mode = none), the dynamisc tpr file
can not be run. It returned the error related to built up the kinetics
energy. But it didn't with nstcomm nsteps, the md still be
Dear Tsjerk.
I see. Many thanks your explanation.
Tuong Vy
2015-06-03 15:44 GMT+09:00 Tsjerk Wassenaar tsje...@gmail.com:
Hi Tuong Vy,
There is no difference in practice except for raising the error. The
developers can't try catching all possible foolish things people could try
with an
Hi...thanks for reply Peter and Mark I tried with temperature coupling
. But things are still same ...
Hi ... Mark would you like to explain this factor to me ??
Thanks and Regards
Lovika
On Tue, Jun 2, 2015 at 2:23 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Hi,
Runaway heating
Hi,
reconstruct both the .mdp (NVT, Md) files as follows-
tc_groups = Protein Non-protein
tau_t =0.1 0.1
ref_t =300 300
This should work.
Soumadwip
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Hi Tuong Vy,
There is no difference in practice except for raising the error. The
developers can't try catching all possible foolish things people could try
with an error. Also, if you think of fooling the program in this way, you
may be assumed to know what you're doing (and why you wouldn't
Dear Tsjerk,
Thanks for your guidance. I add those two command lines you gave in .mdp, but
got the following warnings.
WARNING 1 [file dynamic.mdp]:
Some atoms are not part of any center of mass motion removal group.
This may lead to artifacts.
In most cases one should use one group for
Dear Erik,
As per your suggestion I have tried gmx sasa -tv option to get the
volume of the active site with help of a defined set of residues (17
residues) as defined in the index file. But for all systems, mutants and
wild type enzymes have similar profile of volume throughout the simulation
Dear all,
Is there any method that can fix the center of mass of a group of atoms? I
create a group containing CA atoms of the first residue in each of the three
chains, and want to fix its center of mass only without freeze the CA atoms.
Thanks.
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Gromacs Users mailing list
* Please search
Hi Tuong Vy,
Right. If COMM is removed every N steps and the simulation runs for M N
steps, then COMM will never actually be removed.
Cheers,
Tsjerk
On Jun 3, 2015 4:44 AM, Vy Phan phanvy120...@gmail.com wrote:
Dear all,
I wonder when I set the comm-mode =Linear , and nstcomm
(frequency
Hi Ming Tang,
comm_mode = Linear
comm_grps = CA
Cheers,
Tsjerk
On Wed, Jun 3, 2015 at 9:34 AM, Ming Tang m21.t...@qut.edu.au wrote:
Dear all,
Is there any method that can fix the center of mass of a group of atoms? I
create a group containing CA atoms of the first residue in each of the
Hi,
If you want to preserve the cubic shape of your box you need to choose a
barostat that allows to use the isotropic option. However, when using a
barostat your box size is going to change for sure.
Cheers,
Mario
2015-06-03 10:06 GMT+02:00 Sotirios Dionysios I. Papadatos
Dear Users,
I am doing umbrella sampling of pulling a protein away from a membrane.
Initially I chose reaction coordinate to be the distance between com of the
lower layer of the lipids and of the protein. After weeks of simulations, I
have concluded a better selection of com - as the protein is
Hi,
Does that script support such prehistoric versions of GROMACS?
Mark
On Wed, Jun 3, 2015 at 3:40 PM Rasha Alqus rasha.al...@manchester.ac.uk
wrote:
Dear Gromacs users,
I am trying to run an md of carbohydrate systems in water, the pdb of
carbohydrate produced in glycame builder, files
What does your topology (.top) file look like? And what's the exact command you
are using for grompp?
--
James “Wes” Barnett
Ph.D. Candidate
Chemical and Biomolecular Engineering
Tulane University
Boggs Center for Energy and Biotechnology, Room 341-B
New Orleans, Louisiana 70118
Hi Timofey,
did you check http://ambermd.org/tutorials/basic/tutorial4b/ or
https://code.google.com/p/acpype/wiki/TutorialAcpype4Gromacs
cheers,
Max
On Jun 3, 2015, at 12:24 AM, Timofey Tyugashev
tyugas...@niboch.nsc.rumailto:tyugas...@niboch.nsc.ru wrote:
I'm investigating several
Dear GROMACS users,
I am using the command gmx trjorder with a single frame of a trajectory, to
order the water molecules according to the smallest distance to a molecule. The
system is very small (4400 atoms), however gmx trjorder is taking more than 1
hour to finish!! Is it normal to be so
Hi Ming Tang,
You didn't tell you were pulling... That's a totally different matter. I
guess you want to use two pull groups and pull one with respect to the
other.
Cheers,
Tsjerk
On Wed, Jun 3, 2015 at 11:20 AM, Ming Tang m21.t...@qut.edu.au wrote:
Dear Tsjerk,
Thanks for your guidance. I
Dear Gromacs users,
I am trying to run an md of carbohydrate systems in water, the pdb of
carbohydrate produced in glycame builder, files were loaded in amber to produce
topolgy file and coordinate using glycame force file.
I have run glycam2gmx.pl script to convert files into gromacs ones. I
Dear all,
I am trying to set a coarse-grained MD for the membrane protein.
After solvating, I met an error when running a short energy minimization (
10 steps) before adding ions.
Steepest Descents:
Tolerance (Fmax) = 1.0e+01
Number of steps= 10
Step= 10, Dmax= 2.0e-05 nm,
Hi...Justin Thanks for explaining .. I just want to ask could
there be any other reasons too?? ...Because I have tried it with PME
too...and still I am not getting desired temperature
Thanks and Regards
Lovika
On Wed, Jun 3, 2015 at 5:29 PM, Justin Lemkul jalem...@vt.edu wrote:
Hi every body
I create a covalent bond and now I want to held MD by gromacs,
after holding the following command : grompp -f nvt.mdp -c em.gro -p
topol.top -o nvt.tpr
I confornted to an error:
Fatal error:
Group Protein not found in index file.
Group names must match either [moleculetype]
On 6/3/15 8:52 AM, Rebeca García Fandiño wrote:
Dear GROMACS users,
I am using the command gmx trjorder with a single frame of a trajectory, to
order the water molecules according to the smallest distance to a molecule. The system is
very small (4400 atoms), however gmx trjorder is taking
On 6/3/15 1:35 PM, Poncho Arvayo Zatarain wrote:
Hello: I'm doing Martínez Seara simulation and i want to run this command: echo
0|trjconv -f dppc128_1-nj-ct.xtc -s dppc128_1.tpr -o dppc128_1-nj -ct
-nobox.xtc -box 100 100 100 but it appears: Invalid command line argument: -nobox.xtc Iḿ
Why is this urgent?
Have you tried the suggestions given by the program?
Cheers,
Tsjerk
On Wed, Jun 3, 2015 at 12:08 PM, Antara mazumdar antara.mazum...@igib.in
wrote:
i want to simulate a system having membrane and proteins with pbc=no to
allow surface effects. I use the following settings
Hi,
Probably not - it wasn't parameterised for such usage, and any such
re-deployment would require careful validation . Your background reading on
your choice of model physics is your best guide to doing good physics. :-)
Mark
On Wed, 3 Jun 2015 07:55 Ming Tang m21.t...@qut.edu.au wrote:
Hello: I'm doing Martínez Seara simulation and i want to run this command: echo
0|trjconv -f dppc128_1-nj-ct.xtc -s dppc128_1.tpr -o dppc128_1-nj -ct
-nobox.xtc -box 100 100 100 but it appears: Invalid command line argument:
-nobox.xtc Iḿ using GROMACS 5.0.2 and working in a cluster. What can i
Hi there,
I have two quick questions about the topology file format which I couldn’t find
in the documentary. The semi-colon is giving me some headache. Is it always a
comment which is written after?
First:
[ atoms ]
; nr type resi res atom cgnr charge mass ; qtot
On 6/3/15 1:55 PM, Ebert Maximilian wrote:
Hi there,
I have two quick questions about the topology file format which I couldn’t find
in the documentary. The semi-colon is giving me some headache. Is it always a
comment which is written after?
First:
[ atoms ]
; nr type resi res atom
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