On 27/12/12 16:29, vahid garshasbi wrote:
I run my simulation, now i want to analysis my data. i simulate ion
adsorption on CNT and i want to determine adsorption values in
deffrent concentrations of ion and then plot adsorpttion curve. what
shod i do?
Ask your advisor.
thanks, vahid
--
On 02/10/12 11:53, Justin Lemkul wrote:
Note that you can always select by name rather than number, i.e.:
echo Temperature | g_energy -f ener.edr
Didn't know that, this really saves me a lot of trouble! Thanks Justin!
m.
--
Massimo Sandal, Ph.D.
http://devicerandom.org
--
gmx-users
On 20/09/12 01:35, Peter C. Lai wrote:
then switching to nose-hoover for production
runs (as nose-hoover chains result in the correct canonical distribution)?
I was under the impression that v-rescale resulted in the correct
canonical distribution as well. Is this incorrect?
--
Massimo
Hi,
I am trying to compile Gromacs 4.5.5 with GPU support on Linux. I have
performed the following steps:
export OPENMM_ROOT_DIR=/home//gromacs/OpenMM2.0-Linux64/
mkdir build-gpu
mkdir exec-gpu
cd build-gpu
cmake ../ -DGMX_OPENMM=ON -DFFTW3F_INCLUDE_DIR=/usr/lib/include
On 29/06/12 19:59, Justin A. Lemkul wrote:
Wouldn't it be nice to create a table of standard settings for each
forcefield
in the gmx documentation (with lit references of course)?
Well, anyone is welcome to submit anything they feel would be useful... ;)
I have considered this in the past,
On 27/06/12 05:20, Surya Prakash Tiwari wrote:
Dear Gromacs users,
I am having a very strange problem with Nose Hoover thermostat with
Parrinello-Rahman barostat NPT simulations for a system of an ion of
charge +2 in flexible water molecules. Flexible water is taken from J.
Chem. Phys. 124,
Ok, I am using v-rescale now and the major artefacts seem to be gone, at
least on the very short term (2-3 ns).
It seems grompp should warn that andersen is not a good choice if you're
using CPUs :)
Thanks!
M.
--
Massimo Sandal, Ph.D.
http://devicerandom.org
--
gmx-users mailing list
On 15/06/12 13:02, Justin A. Lemkul wrote:
In the existing code for version 4.5.5, it seems the Andersen keyword
is accepted but there is no mention of its use in update.c or
coupling.c, suggesting to me that it's a ghost parameter that does
nothing. There should be some indication in the .log
Ok, I tried some of your suggestions and the Coulomb-SR energies still
fall down very quickly.
I wonder if:
On 13/06/12 16:59, Justin A. Lemkul wrote:
4. What happens when you use the Andersen thermostat? That's not
implemented yet for CPU calculations (though it was recently pushed into
the
Hi,
I am trying to prepare a simple system for tests with CUDA. My guinea
pig is the lysozyme system from this tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html
but I prepared it using the AMBER99sb-ildn force field and the SPCE
water
Looking deeper, it seems most of the energy loss is concentrated in the
SR Coulomb interactions:
Energy Average Err.Est. RMSD Tot-Drift
---
Bond2771.28 17
On 13/06/12 16:36, Justin A. Lemkul wrote:
Here, you're not preserving any of the previous state information.
You're picking up from 2 ns, but not passing a .cpt file to grompp - the
previous state is lost. Is that what you want? In conjunction with
gen_vel = no I suspect you could see some
On 13/06/12 16:59, Justin A. Lemkul wrote:
On 6/13/12 10:48 AM, ms wrote:
On 13/06/12 16:36, Justin A. Lemkul wrote:
Here, you're not preserving any of the previous state information.
You're picking up from 2 ns, but not passing a .cpt file to grompp - the
previous state is lost
On 27/03/11 23:02, Adam Herbst wrote:
Hi all,
I have seen a few posts on gmx-users indicating a desire to treat
certain atom groups as rigid bodies in MD simulations. I just started
implementing this, and so far I have it working for translational forces
(not rotation, though this should be
On 29/01/11 05:08, Matt Chan wrote:
Perfect. This is great reading.
Thanks for the pointers Mark.
Matt
On 01/28/2011 06:50 PM, Mark Abraham wrote:
On 29/01/2011 9:57 AM, Matthew Chan wrote:
Hi,
I'm a first time GROMACS user. I've got 2 questions, which I'll ask
in separate emails. The
On 30/01/11 15:41, David van der Spoel wrote:
My question is what effect does running a simulation with a charged
system have? I recall reading that something related to PME
calculations assumes the system is neutral, but it did not specify
whether it was referring to MD or EM. From the mailing
Hi,
While I understand that all non-bonded gmx potential shapes are intended
to be spherically symmetric, for a project of mine it would be helpful
to be able to have a non-bonded pair potential which is
geometry-dependent (that is, depending on the angle between 3 atoms).
Has anything
On 07/01/11 02:17, yuanyuan wang wrote:
dear all,
I am doing a simulation that have many chains in a box , and I can
find a center for them after serval tries.
I use almost every option of trjconv,-pbc mol,atom,res,whole,nojump ,
-ur compact, -center , -box to got bigger
On 07/01/11 17:00, mustafa bilsel wrote:
Justin,
Are you sure? I installed 4.5.3 and tried Methanol, MTH, MeOH.
Nothing changed. I suggest you to try it by yourself.
Don't try to remind people the help rules.
JUST HELP OR DONOT HELP.
We're not at your orders and shouting at people who try to
On 29/12/10 21:57, chris.ne...@utoronto.ca wrote:
That sounds reasonable. I don't like hidden options except for when they
are associated with manuscripts that have not yet been published.
As a young Gromacs user and an old free software user and developer,
I wholeheartedly disagree with
On 29/12/10 23:47, Justin A. Lemkul wrote:
I think the root problem boils down to a lack of documentation of this
feature. For most routine use, -maxwarn should not be used, similar to
-missing with pdb2gmx.
Yes, but it depends. In my systems I routinely have to use both to get
the system
On 30/12/10 01:07, Justin A. Lemkul wrote:
It sounds very much like your systems are in the minority - those for
which -maxwarn is essential :)
Oh yes. But... you don't want to discriminate minorities!! :D
What I meant was that -maxwarn allows a user to casually bypass that
which grompp is
On 25/12/10 02:12, Qin Qiao wrote:
Thanks a lot!
It says Nose-hoover coupling generates the correct canonical ensemble, and
that's the reason why I used it. I wonder whether v-rescale can also get the
correct ensemble. Could you tell me?
As far as I know v-rescale should generate a correct
On 25/12/10 02:12, Qin Qiao wrote:
Thanks a lot!
It says Nose-hoover coupling generates the correct canonical ensemble, and
that's the reason why I used it. I wonder whether v-rescale can also get
the
correct ensemble. Could you tell me?
As far as I know v-rescale should generate a correct
On 24/12/10 10:36, David van der Spoel wrote:
On 2010-12-24 11.04, Mark Abraham wrote:
On 22/12/2010 5:44 PM, Qin Qiao wrote:
Dear all,
I posted yesterday but didn't get answer..I guess it's due to my wrong
approach to ask. I would like to explain more and hope I would get
your help.
I'm
On 24/12/10 12:26, David van der Spoel wrote:
I'm not an expert, but isn't Berendsen usually not used because it
doesn't give a correct ensemble? I may be partial because I personally
know Giovanni Bussi, but it seems from what I've heard that v-rescale is
the best choice usually.
V-rescale
On 07/12/10 03:06, nishap.pa...@utoronto.ca wrote:
Quoting ms deviceran...@gmail.com:
I did two different simulation. One with van der Waals attractive term
and one without van der Waals attractive term. And so to see the
difference between the LJ potential between the two simulation I wanted
On 06/12/10 23:26, nishap.pa...@utoronto.ca wrote:
Quoting Justin A. Lemkul jalem...@vt.edu:
I actually want to plot my simulation with ad without the attractive
term C6 of van der Waals and superimpose them to see the difference.
The expression plot my simulation makes no sense. You don't
On 05/12/10 10:39, swagata chakraborty wrote:
I was trying to run MD simulation of my protein in DMSO. I used the force
field ffG53a6 and did the energy minimization after solvating the protein in
DMSO box.
But after solvating in DMSO, the structure is changing. My protein is a
homodimer and the
On 05/12/10 13:20, Justin A. Lemkul wrote:
ms wrote:
On 05/12/10 10:39, swagata chakraborty wrote:
I was trying to run MD simulation of my protein in DMSO. I used the
force
field ffG53a6 and did the energy minimization after solvating the
protein in
DMSO box.
But after solvating in DMSO
On 05/12/10 19:41, Justin A. Lemkul wrote:
Please keep all Gromacs-related correspondence on the gmx-users list. I
am not a private help service.
I do not do polymer simulations, nor do I have any real clue as to how
to help you, aside from suggesting the following, which may or may not
be
Hi,
Sorry for the offtopic but my google-fu is apparently abandoning me. I
am looking for a fast way to generate random coil protein configurations
to use as startpoints for several simulations I'd like to do.
All I managed to find is:
- FOLDTRAJ which seems unavailable and discontinued
-
On 05/12/10 00:26, Mark Abraham wrote:
Sorry for the offtopic but my google-fu is apparently abandoning me. I am
looking for a fast way to generate random coil protein configurations to use as
startpoints for several simulations I'd like to do.
All I managed to find is:
- FOLDTRAJ which seems
On 27/11/10 17:49, Sai Pooja wrote:
Hi,
I am running a script that uses mdrun of gromacs and does replica exchange
(not using -replex). The reason is that I want to use different table files
for different replicas. However, it seems that I cannot supply unique table
names. For example, if I
On 27/11/10 17:49, Sai Pooja wrote:
Hi,
I am running a script that uses mdrun of gromacs and does replica exchange
(not using -replex). The reason is that I want to use different table files
for different replicas. However, it seems that I cannot supply unique table
names. For example, if I
On 24/11/10 02:47, Mark Abraham wrote:
On 24/11/2010 5:04 AM, ms wrote:
On 23/11/10 17:00, Mark Abraham wrote:
There is no general solution for bonds visualized on a
single set of coordinates, however - over a trajectory, either molecules
appear to diffuse out of the box, or appear to break
On 23/11/10 09:43, leila separdar wrote:
I am beginner with gromacs I want to simulate a system of 100 Argon atom
with Lennard Jones force field but I do not know how to make .itp file I
have made this lines but it made error. could anybody hep me?
Telling what errors come out would help.
[
Dear GROMACS users,
I am trying to visualize a trajectory with hundreds of peptides which
come and go out and in the faces of the periodic box. Problem is, when
they cross the periodic boundary, the visualization software (I tried
both VMD and PyMol) create visual artefacts by visualizing
Ok, I can update this situation (see below quote):
On 18/10/10 03:30, Mark Abraham wrote:
And then, I read on the Gromacs website *this*
http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints
2. The manual is a bit unclear about whether this type of
dihedral restraint is stable for
On 23/11/10 17:00, Mark Abraham wrote:
If you only want a snapshot, then simply write a single chosen frame to
a .gro or .pdb using trjconv. Load only that into VMD, and it won't
generate PBC-crossing bonds.
If you want a movie, then there I seem to recall that there is a VMD
option to generate
On 23/11/10 17:00, Mark Abraham wrote:
If you want a movie, then there I seem to recall that there is a VMD
option to generate bonds for each frame, and not to use those from the
first frame. Ask their mailing list. Such bonds will not traverse the
PBC, obviously.
Just for the record: It seems
On 23/11/10 17:00, Mark Abraham wrote:
If you only want a snapshot, then simply write a single chosen frame to
a .gro or .pdb using trjconv. Load only that into VMD, and it won't
generate PBC-crossing bonds.
If you want a movie, then there I seem to recall that there is a VMD
option to generate
On 23/11/10 21:42, Sai Pooja wrote:
Hi,
I run a simulation of a protein in water(tip3p) system using charmm
forcefield. I have specified the following energy groups:
Protein SOL and energy group tables Protein SOL SOL SOL. I set Coulombtype
to User and VdW to Cut-off. I then generate tables as
On 22/11/10 11:09, mohsen ramezanpour wrote:
Dear All
I am searching for a tutorial for learning how to do protein folding with
Gromacs.
Do any one know such tutorials?
Please let me know them.
I don't think so because managing to fold a protein in a MD simulation
is no easy task. In
On 09/11/10 21:36, Justin A. Lemkul wrote:
I am doing REMD simulations of multiple homopolymeric peptides in a
PBC box, in vacuum (it's a custom coarse grain). GROMACS 4.0.5. I want
to analyze features of the system that require to use g_gyrate to find
out the moments of inertia of the system,
On 09/11/10 21:36, Justin A. Lemkul wrote:
There are numerous -pbc options with trjconv; have you tried others? I
have never had luck with -pbc nojump actually working, and -pbc atom
provides no guarantee that molecules will be properly reconstructed.
Using -pbc mol -center is often a much
On 10/11/10 21:34, Justin A. Lemkul wrote:
ms wrote:
On 09/11/10 21:36, Justin A. Lemkul wrote:
There are numerous -pbc options with trjconv; have you tried others? I
have never had luck with -pbc nojump actually working, and -pbc atom
provides no guarantee that molecules will be properly
On 10/11/10 22:28, Justin A. Lemkul wrote:
First, let me see if I understand it correctly. From your explanation
(and intuition), it seems that the issue is that center of mass in a
periodic environment is ambiguous -there are always (at least) two
alternate configurations that have the center
Hi,
I am doing REMD simulations of multiple homopolymeric peptides in a PBC
box, in vacuum (it's a custom coarse grain). GROMACS 4.0.5. I want to
analyze features of the system that require to use g_gyrate to find out
the moments of inertia of the system, for example.
I understand g_gyrate
On 06/11/10 07:46, Mark Abraham wrote:
On 6/11/2010 4:02 PM, bharat gupta wrote:
Hi all ,
Whenever i am running the genbox command I am getting the following
error :-
genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
:-) G R O M A C S (-:
Segmentation fault (core
On 18/10/10 13:06, Mark Abraham wrote:
On 18/10/2010 10:53 PM, ms wrote:
On 18/10/10 03:30, Mark Abraham wrote:
Mark,
Thanks a lot for cc'ing me the bugzilla report. Do you think it is
related to the problems I have? (well, for sure bugs can't help, but...)
thank you!
m.
--
Massimo
On 27/09/10 21:18, Sai Pooja wrote:
Thanks M!
I am using the standard 6-12 tables available with the gromacs package. For
-table and -tablep options to start with.
I want to understand 1 thing. The forcefield files and the topology file
specifies sigma and epsilon parameters. If I change the
On 18/10/10 03:30, Mark Abraham wrote:
To enforce chirality in such a toy, I thought that a simple
(naive?) but functional idea could be that of enforcing a not-
too-hard and wide-bottomed dihedral restrain on the phi angle,
like that:
[ dihedral_restraints ]
; ai ajak
al type label
On 18/10/10 03:30, Mark Abraham wrote:
To enforce chirality in such a toy, I thought that a simple
(naive?) but functional idea could be that of enforcing a not-
too-hard and wide-bottomed dihedral restrain on the phi angle,
like that:
[ dihedral_restraints ]
; ai ajak
al type label
On 18/10/10 12:49, vinothkumar mohanakrishnan wrote:
Dear Mark
I generated the topology using pdb2gmx using dce.pdb. i checked the .top
file and i contains necessary .itp files. the error message that i get is
given below. any help is highly appreciated.
What Mark meant is that you should
On 18/10/10 13:06, Mark Abraham wrote:
On 18/10/2010 10:53 PM, ms wrote:
On 18/10/10 03:30, Mark Abraham wrote:
To enforce chirality in such a toy, I thought that a simple
(naive?) but functional idea could be that of enforcing a not-
too-hard and wide-bottomed dihedral restrain on the phi
On 18/10/10 13:06, Mark Abraham wrote:
On 18/10/2010 10:53 PM, ms wrote:
On 18/10/10 03:30, Mark Abraham wrote:
To enforce chirality in such a toy, I thought that a simple
(naive?) but functional idea could be that of enforcing a not-
too-hard and wide-bottomed dihedral restrain on the phi
On 18/10/10 13:12, Chen wrote:
At 2010-10-18 16:38:30??David van der Spoelsp...@xray.bmc.uu.se wrote:
On 2010-10-18 06.56, chris.ne...@utoronto.ca wrote:
Generally, forcefields are not parameterized for temperatures other than
298K, so simulations are not expected to reproduce the expected
Hi,
It's a bit long but bear with me if you can. I'm getting quite mad with
this. Thanks :)
Now. I am using Gromacs (4.0.7 currently) to create a custom
coarse-grained, no-solvent MD peptide model -one that contains the
backbone but has only C-alphas, no side chains.
To enforce chirality
On 14/10/10 08:51, mohsen ramezanpour wrote:
Dear All
I am running a seamulated anneaking + MD in my cluster.
I had done it for 2 times.
but my results are not as i expect.
I have attached my md.mdp file for you,I don't know which part of it is
wrong.
what i like to result is to change
On 14/10/10 17:32, XAvier Periole wrote:
Then I am not a fan of implicit solvents so I'll pass on that, then for the
coarse grained FF the OPEP FF seem to be fine for your application.
You can also look at the ones from Deserno's group (bereau-2009) and
from Feig's group (primo: gopal-2010). I
On 12/10/10 00:33, Mark Abraham wrote:
I have heard (read: read on random blogs here and there) that on
Intel compiling GROMACS with icc instead of gcc can bring up to
50% performance improvement.
If you are referring to this post
Dear users,
I am currently using GROMACS 4.0.7 with a custom force field I developed
(coarse-grained model I am developing). I want to jump to 4.5 , but I
wonder if something in the syntax of force fields has changed from 4.0.x
to 4.5 :just to know in advance if I have to change the files or
On 11/10/10 15:45, Justin A. Lemkul wrote:
I am currently using GROMACS 4.0.7 with a custom force field I
developed (coarse-grained model I am developing). I want to jump to
4.5 , but I wonder if something in the syntax of force fields has
changed from 4.0.x to 4.5 :just to know in advance if I
Dear gmx users,
I have heard (read: read on random blogs here and there) that on Intel
compiling GROMACS with icc instead of gcc can bring up to 50%
performance improvement.
Since I always used gcc compiled GROMACS, I'd like to know:
- Is this true?
- If yes, can anybody help me in doing so?
On 21/09/10 20:45, Sai Pooja wrote:
I wanted to change the interactions between the Protein and Solvent so I
tried using tables with the potential function scaled by a constant value. I
wanted to use this in combination with forcefield parameters (charmm). I
changed the combination rule in the
Hi Justin,
On 17/09/10 11:51, Justin A. Lemkul wrote:
Also in section 5.3 is the procedure for how to use REMD data, but I
don't think it will ever accomplish what you want. The input into WHAM
would be energies, not RMSD vs. R(g), as you initially stated as your
goal. You can easily build free
On 18/09/10 18:32, Justin A. Lemkul wrote:
Hi Justin,
On 17/09/10 11:51, Justin A. Lemkul wrote:
Also in section 5.3 is the procedure for how to use REMD data, but I
don't think it will ever accomplish what you want. The input into WHAM
would be energies, not RMSD vs. R(g), as you initially
On 30/08/10 01:19, Justin A. Lemkul wrote:
Is it wrong?
No, exactly as I have explained in the follow-up message to this post. I
was trying to tie this concept into the OP's original observations and
attempts to quantify his results with respect to energetics of
individual molecules.
On 26/08/10 19:56, chris.ne...@utoronto.ca wrote:
Natalie:
It would also be a good idea for you to ensure that your supervisor
knows how difficult it is to learn and correctly apply these methods. If
they think that a person can learn linux and gromacs and the gromacs
pull code in a short
On 29/08/10 19:39, Justin A. Lemkul wrote:
When dividing the energy of a system by the number of molecules (in a
homogeneous system), you are extracting what I believe is commonly
referred to as configurational energy which, for relatively simple
systems, should converge fairly quickly. The
On 17/08/10 22:36, Justin A. Lemkul wrote:
There is no way to limit PME to certain ranges. It is a method for
solving infinite sums. Usually PME is a poor choice for in vacuo
simulations and the like, since there's nothing to be done for most of
the simulation box.
This interests me -I've
On 12/08/10 15:25, Alexandre Suman de Araujo wrote:
I'm simulating a system composed by a protein centered in a sphere of
water in vacuum.
The water molecules are kept within a virtual sphere with position
restrains between oxygen atom and a dummy atom fixed at the center of
the sphere. The
On 13/08/10 18:30, Alexandre Suman de Araujo wrote:
I am just curious but... why are you doing actually all of this
instead of using a normal periodic solvent box?
The idea is to have less water molecules and, consequently, faster
simulations.
I thought about that, but I guessed you can use
On 05/08/10 17:37, Samrat Pal wrote:
Hi all,
I have been running a simulation of 200 ns length and it suddenly
stoped at 67 ns showing the following line -
Received the TERM signal, stopping at the next step
I have checked the time steps properly and there is no error. What should I
On 06/08/10 13:59, leila karami wrote:
Hi gromacs users
I obtained pdb input file for gromacs from STRAP program. this pdb
file coantains protein and dna. this pdb file was obtaind form
superposition of 2 other pdb files. there is one problem: when I see
pdb file obtained from STRAP program by
On 03/08/10 17:32, Jafar Azamat wrote:
When the program runs by
pdb2gmx Option, the file X.top doesnot any information about force
constant X.pdb file and I enter informations handling in this file.
Your question does not make any sense, can you try to rephrase it?
In addition,How can I make
On 01/08/10 22:03, Rossen Apostolov wrote:
On 07/31/2010 10:17 PM, ms wrote:
As a young GROMACS user, thank you a lot! I just want to ask:
On 30/07/10 20:20, Rossen Apostolov wrote:
* Efficient Generalized-Born implicit solvent support including the
Still/HCT/OBC-models to compute the Born
As a young GROMACS user, thank you a lot! I just want to ask:
On 30/07/10 20:20, Rossen Apostolov wrote:
* Efficient Generalized-Born implicit solvent support including the
Still/HCT/OBC-models to compute the Born radii, a novel way of
tabulating the generalized Born-interaction formula for
On 24/07/10 01:24, Samrat Pal wrote:
I am trying to do some folding simulations in GROMACS. I saw few mails in the
list stating that implicit water model will be available in GROMACS 4.0 version.
However, I have not found anything on the implicit model in the manual. I am
currently using GROMACS
On 19/07/10 23:18, Lanyuan Lu wrote:
From our group's experience, there is a critical point for dramatic
performance drop when one uses two many tables. The possible reason is that
the size of tables exceeds the cache size. However, this only happens when
the number of tables is beyond
On 19/07/10 17:25, Sai Pooja wrote:
Thanks Lanyuan.
Can one use fewer processors than the number of replicas?
My 0.02 £: I never did REMD, but, as far as I know, putting more
processes on the same processor in any kind of parallel computing is
asking for your performance to grind to a
Hi,
Do you know where can I find some information on how using tabulated
potential affects gmx performance, and how? I have to decide how to
project a custom model but I don't want to calculate dozens of tables
only to find that gmx grinds to a halt.
thanks!
M.
--
gmx-users mailing list
On 19/07/10 17:32, Da-Wei Li wrote:
It will be very little from my experience. Remember that the dominate
part is the non-bonded force calculation.
Well, that's exactly what I tabulate.
dawei
On Mon, Jul 19, 2010 at 12:22 PM, msdeviceran...@gmail.com wrote:
Hi,
Do you know where can I
On 19/07/10 18:32, Da-Wei Li wrote:
I remember the manu states that it won't cost too much compared with
standard potential function form.
Well, I find in the manual exactly the opposite:
Note that table lookup is significantly slower than computation of the
most simple Lennard-Jones and
On 18/07/10 20:21, Samrat Pal wrote:
I have been doing the pull simulations with your scripts and that are running
fine. Thanks a lot. Can I use implicit solvent model in pulling simulations? I
have gone through the mailing list and I found that it is not recommended (I may
be wrong). Please
I would highly recommend you to learn some language like Python or Ruby
and use it for this kind of stuff. More flexible and more maintainable
than shell scripting, and not harder.
cheers,
m.
On 16/07/10 12:03, Hassan Shallal wrote:
Thanks alot Rui for the hint
On 05/07/10 16:27, Justin A. Lemkul wrote:
ithu wrote:
Dear gromacs Users,
I found this in the web, but I wanted to know if there exists the
possibility now of using implicit solvent efficiently.
Implicit solvent will be supported in the upcoming release.
Since it interests me too...
On 02/07/10 21:15, David van der Spoel wrote:
On 2010-07-02 22.00, Arthur Roberts wrote:
Hi, all,
Is there a way to protonate small molecules with gromacs without editing
ffgmx2.hdb file?
No, but try the prodrg server.
(just to be sure) Can't one modify the .gro and .top by hand?
Massimo
Hi,
I am trying -with no avail- to have a way to view a movie of a GROMACS
trajectory with the secondary structure being updated automatically
frame by frame (that is, changing colour and/or appearance accordingly
during the trajectory).
If I view the trajectory with VMD, even if I turn on
On 16/06/10 19:07, Chris Neale wrote:
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/sscache/
Thanks a lot! I'll give it a spin ASAP.
cheers,
m.
-- original message --
Hi,
I am trying -with no avail- to have a way to view a movie of a GROMACS
trajectory with the secondary
On 02/06/10 18:48, Morteza Khabiri wrote:
Dear users
I have a dimer protein in the water box. It was run for 30ns.
during the simulation dimer split to two monomer. This things happen bc of
PBC. ( I checked it by vmd pbc option )
to have a two monomer together during trajectories (for
On 11/05/10 05:17, sonali dhindwal wrote:
Thanks a lot for your replies. I will start reading this and learning MD.
I really want to say that this forum is an excellent source of help.
Thanks for all your help.
Another book you may want to read is Understanding molecular
simulation, by Daan
hello
i got the warning as the Warning: 1-4 interaction between 246 and 251 at
distance 4.991 which is larger than the 1-4 table size 2.400 nm
These are
ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
plz can anybody tl me if i get step 0 segmentation fault in md run of
position restrain step, what does it mean and how can it be solved. plz help
me
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WITH REGARDS
VANI
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jampani srinivas ha scritto:
Dear Berk,
I am sorry if i am confusing you with my poor description of problem,
actually I have submitted simulation with two temperature coupling groups (i
think you already know that from our earlier conversations) and found that
there is a continuous
David van der Spoel ha scritto:
On 2/1/10 4:32 PM, ms wrote:
Hi,
Sorry for the offtopic but Google/literature quick search is not helping
and I'd like to have some more informed opinion.
To my understanding, GROMACS isn't capable of discontinuous molecular
dynamics. Is there any more
David van der Spoel ha scritto:
On 2/2/10 4:43 PM, ms wrote:
David van der Spoel ha scritto:
On 2/1/10 4:32 PM, ms wrote:
Hi,
Sorry for the offtopic but Google/literature quick search is not
helping
and I'd like to have some more informed opinion.
To my understanding, GROMACS
Hi,
Sorry for the offtopic but Google/literature quick search is not helping
and I'd like to have some more informed opinion.
To my understanding, GROMACS isn't capable of discontinuous molecular
dynamics. Is there any more-or-less standard software package for that?
thank you!
m.
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gmx-users
Hi,
In my odyssey with tabulated potentials, I would like to be double-sure
to know that, while CA-CA interactions follow the table I give as input,
other interactions *don't*.
How can I check which table is gromacs using for which interaction?
Thank you,
M.
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