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 simp
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
--
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 m
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 ins
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 los
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 4
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 listgmx-
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
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, 02
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,
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
-DFFTW3F_LIBRARIE
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 Sand
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 mailing
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 sta
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 fo
Hi,
Clarification: I may not be able to help you directly but I can suggest
you which information you should perhaps give us to enable people more
knowledgeable than me to help.
On 24/09/10 17:33, Sai Pooja wrote:
I use combination rule 1; but I also define all tabulated interactions for
all
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 i
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 h
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 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
(http://kent-vandervelden.blogspot.com/2010/08/optimization-of-
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 tempretur
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 a
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 i
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 phi
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 phi
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 copy
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 Spoel" 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
properties (like b
On 18/10/10 14:26, #ZHAO LINA# wrote:
Hi,
1. For those intrinsically disordered proteins, the sequence is known, how the
simulations will be set up, I mean, the first PDB will be needed, how to get
this one? (Ideally, not necessarily to be practical)
2. suppose I got a PDB, there were several
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.
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 co
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 dumpe
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 i
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, fo
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 bette
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
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 theory,
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 nons
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 u
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 s
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 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 supp
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 supp
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
- the
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 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, the
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 rele
On 06/12/10 23:26, nishap.pa...@utoronto.ca wrote:
Quoting "Justin A. Lemkul" :
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 plot a
simula
On 07/12/10 03:06, nishap.pa...@utoronto.ca wrote:
Quoting ms :
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
to plot the LJ
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 doin
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 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 ens
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 e
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 h
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 rig
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 al
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 box
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
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 -offi
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 firs
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
Rossen Apostolov ha scritto:
> Hi,
>
> I made some updates and incorrectly changed the permissions.
> You should be able to search now even without logging in.
>
I jump in this thread to ask: I've notice that there are a huge amount
of broken links in the new Gromacs pages. This is bad for me si
Justin A. Lemkul ha scritto:
>
>
> ms wrote:
>> Rossen Apostolov ha scritto:
>>> Hi,
>>>
>>> I made some updates and incorrectly changed the permissions.
>>> You should be able to search now even without logging in.
>>>
>>
>>
Justin A. Lemkul ha scritto:
Google cache and the PDF manual are my friends, but any hint on
where to
retrieve the pages that are still linked as being on the old wiki is
appreciated.
>>> The old wiki has been taken down. You can search the Gromacs site (not
>>> the mailin
Justin A. Lemkul ha scritto:
> ms wrote:
>> Justin A. Lemkul ha scritto:
>>>>>> Google cache and the PDF manual are my friends, but any hint on
>>>>>> where to
>>>>>> retrieve the pages that are still linked as being on the old wiki
Justin A. Lemkul ha scritto:
>>> The old wiki has been taken down. You can search the Gromacs site
>>> (not
>>> the mailing list) for relevant content, until all the links are
>>> working. There has been some discussion about this lately; it will
>>> be a
>>> very time-con
Justin A. Lemkul ha scritto:
>> Well, I'd like to help with fixing the links whenever I find a broken
>> one, but it seems I can't edit. :)
>>
> You have to register as a contributer and log in (top right of the
> Gromacs page).
I registered yesterday and I am logged in, b
Rossen Apostolov ha scritto:
> Hi,
>> I registered yesterday and I am logged in, but perhaps I am not
>> registered "as contributor"...
>>
> I added you as a contributor. Thanks for offering to help!
>
> New users are only "viewers" by default to avoid giving instant write
>
Hi,
First of all, I am new to Gromacs and quite new to the MD field (I had a
read of the Daan-Frenkel book and played very little with custom CG
models - I used to be an experimental guy), so please bear with me if
questions happen to be naive.
My aim is to re-implement a formerly standalone CG m
Justin A. Lemkul ha scritto:
>> My aim is to re-implement a formerly standalone CG model by mean of gmx.
>> It seems that gmx is well suited to the task; however I understand that
>> there is an incredible number of pitfalls where a newbie fall in.
>>
>> I am currently reading and re-reading the ma
Hi,
I am a gmx newbie, so please don't bite too much! :)
Learning gmx, I am experimenting with simulations with multiple
identical small chains. What I did was:
- I generated the peptides with pymol
- Generated a .gro with pdb2gmx
- Used editconf to create translated copies
- Stitching them toge
Mark Abraham ha scritto:
> ms wrote:
>> Hi,
>>
>> I am a gmx newbie, so please don't bite too much! :)
>>
>> Learning gmx, I am experimenting with simulations with multiple
>> identical small chains. What I did was:
>>
>> - I generated th
Mark Abraham ha scritto:
> ms wrote:
>> Mark Abraham ha scritto:
>>> What do you want the chain identifiers for? I'm not aware of a
>>> post-pdb2gmx purpose that they might serve.
>>
>> This is where my naivety probably enters in: Analysis programs work
Hi,
I need to implement a FF which includes directional hydrogen bonding. It
seems however, to my understanding, that Gromacs has no simple way to
include an explicitly directional contribution. All I can find is that,
in standard force fields, h-bond terms are implicitly described by
coulombic an
Hi Mark,
Thanks for your answer.
Mark Abraham ha scritto:
> There's nothing directional about the physics of a hydrogen bond, unless
> your model makes it so. There'd be nothing intrinsically valid or
> invalid with that either, so long as you parameterized the force field
> under that assumption
Mark Abraham ha scritto:
> ms wrote:
>> Ok, the problem is that I want to re-implement a quite minimal
>> coarse-grained FF (so no explicit solvent etc.) and a directional
>> interaction would be useful.
>
> Well you should consider alternative software, then.
I see.
Hi,
I am using g_mindist to see how close get C-alphas to each other in my
chains. What I do is selecting C-alpha two times when prompted. I have
only a quick question, just to be sure: The script doesn't take into
account the distance between *neighbouring C-alpha*, isn't it?
thanks!
m.
__
Hi Justin,
thanks for your answer
Justin A. Lemkul ha scritto:
>> I am using g_mindist to see how close get C-alphas to each other in my
>> chains. What I do is selecting C-alpha two times when prompted. I have
>> only a quick question, just to be sure: The script doesn't take into
>> account the
Hi,
I wonder if there is an easy way I am missing to get a density histogram
from the Ramachandran plot over a trajectory as outputted by g_rama. All
I see are big, uniform black blobs and they're not helpful, because with
tons of data points a density plot would be much more informative. Thanks!
Hi,
I would like to understand a basic question about the usage of tabulated
potential for non-bonded interaction. If I use an arbitrary function and
I write a table for it, is the functional shape then applied to *all* my
atoms, or can I specify which ones use the tabulated potential -and how?
T
Mark Abraham ha scritto:
> ms wrote:
>> Hi,
>>
>> I would like to understand a basic question about the usage of tabulated
>> potential for non-bonded interaction. If I use an arbitrary function and
>> I write a table for it, is the functional shape then appli
I have a further question about tabulated non-bonded potentials.
The manual (6.7.2) says:
"It is also possible to combine a standard Coulomb with a modified LJ
potential... The table file must always contain the 7 columns however,
and meaningful data (i.e. not zeroes) must be entered in all column
Dear Gromacs users,
I am a little new fellow in this community, and many things still I
don't know.
I am trying to parametrize a coarse-grained FF for polymer simulations,
without solvent. A collegue of mine advised me, just to be sure, to
check for possible energy leak artefacts. To do that he t
Hi,
I am really having a hard time figuring out how to use tabulated
potentials correctly.
In general, the information on how to use tables is sparse and scattered
in several points of the manual (ch.5, ch.7, ch.6.7...) -I hope to write
a short howto in the wiki once I get this working, but now I
Dear Mark,
First of all, thanks for your patient and thorough reply!
Mark Abraham ha scritto:
> Yeah, that's an unfortunate fact of life. The manual can't be organized
> so that everybody finds all the information they want in one location
> with the detail they need right now. Using tabulated po
Mark Abraham ha scritto:
> Sorry, I was a bit incomplete last night. Charge groups are the
> fundamental unit for neighbour-searching (3.4.2) to construct lists of
> charge groups for nonbonded interactions, which determine lists of
> atom-atom interactions. However, the nonbonded interactions are
Hi,
As per the title. I need to understand what is the difference to help
myself debug my inane efforts at CG parametrization. LJ(1-4) I think is
clear (non bonded, non-coulombic interactions between 1-4 pairs
described in the topology), but about the rest?
thanks!
m.
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Mark Abraham ha scritto:
> ms wrote:
>> Hi,
>>
>> As per the title. I need to understand what is the difference to help
>> myself debug my inane efforts at CG parametrization. LJ(1-4) I think is
>> clear (non bonded, non-coulombic interactions between 1-4 pairs
&
Justin A. Lemkul ha scritto:
As per the title. I need to understand what is the difference to help
myself debug my inane efforts at CG parametrization. LJ(1-4) I think is
clear (non bonded, non-coulombic interactions between 1-4 pairs
described in the topology), but about the re
Mahendran E ha scritto:
> hi all
>
> while running gromacs in parallel environment
>
> i am getting the following command,
>
> the command i used is
>
> mpirun -np 5 -machinefile machinefile /usr/local/gromacs/bin/mdrun_mpi -s
> fws_md.tpr -o fws_md.trr -c fws_pmd.pdb -g md.log -e md.edr
>
>
>
pawan raghav ha scritto:
> Hi,
>
> Please tell me how to install GRACE source files to execute xmgrace command
> to visualize 2D graph. I am unable to installed it as read from tutorial.
> please help me as I am in need.
>
Contact the xmgrace mailing list.
m.
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