From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of gmx-users-requ...@gromacs.org [gmx-users-requ...@gromacs.org]
Sent: Wednesday, May 16, 2012 2:59 PM
To: gmx-users@gromacs.org
Subject: gmx-users Digest, Vol 97, Issue 120
Sen
Dear all gromacs users,
I tried the grompp and i got the
following error.
Fatal error:
moleculetype CU1 is redefined.
Is there any explanation why is thid happening?
I would appreciate any help. Iam new in using MD and gromac in particular.
Suryanarayana Se
Hi all together,
I am testing the 4.6 dev version of gromacs with heterogeneous
acceleration (force field: amber99-ildn) on a 95 residue protein (all
atom model) in SPCE and run into major troubles using in the .mdp file
option constraints = hbonds with the default lincs parameters. The
system is
Hi Seera
As the error message is telling you, the molecule type CU1 is defined
more than once along your topology. Check it, locate the [ moleculetype
] sections and verify that CU1 is defined only once. If that does not
solve the problem, you can post you topology here so that we can try to
Hi Erik,
your examples on H-bond acfs are interesting. I'm wondering about the
"distinct features which are non-exponential" in your examples. What do
you mean exactly? Could these features be due to rare (H-bonding)
events, or in other words to poor sampling?
Intuitively, I'd say that the inte
Hi there,
Is there an option in pdb2gmx that when generating the top/itp file, it
could show the parameters explicitly? e.g.:
Instead of:
[ dihedrals ]
; aiajakal functc0c1c2
c3
5131112 4
11151314 4
Respected Gromacs Developers,
I am Rethinamalliga Gunasekaran, using different modules of GROMACS for my
project and its guiding me profoundly.
Thank you for developing such a tool and also for your well guiding
tutorial.
I need to perform Protein Protein simulation and I tried with GROMACS with
Hi,
I swapped two arguments to a function call. I have fixed it and it should
appear soon
in the public repository. You can find the fix below.
Cheers,
Berk
diff --git a/src/kernel/topshake.c b/src/kernel/topshake.c
index c5f3957..78961c5 100644
--- a/src/kernel/topshake.c
+++ b/src/kernel/to
Have you checked MARTINI website?
http://md.chem.rug.nl/cgmartini/index.php/downloads/force-field-parameters
Dariush
Kind Regards,
Dariush Mohammadyani
Department of Structural Biology
University of Pittsburgh School of Medicine
Biomedical Science Tower 3
3501 Fifth Avenue
Pittsburgh, PA 15261
Hi Dariush,
I've checked but it seems there no parameters for my detergent.
Actully there are parameters for the polar head and the lipidic tail, so it
is worth trying to merge them
to have the correct representation!
Francesco
2012/5/21 Dariush Mohammadyani
> Have you checked MARTINI website?
Sure, this is the way to make forcefield for your molecule. Also, please
check literature.
Good luck,
Dariush
On Mon, May 21, 2012 at 9:26 AM, francesco oteri
wrote:
> Hi Dariush,
> I've checked but it seems there no parameters for my detergent.
>
> Actully there are parameters for the polar h
The actual parameters are listed in the ffbonded.itp file located in the
folder of the corresponding force field, under [ dihedraltypes ] section.
Javier
El 21/05/12 14:43, Alan escribió:
Hi there,
Is there an option in pdb2gmx that when generating the top/itp file,
it could show the paramet
Hi all,
I am planing to use Gromacs for the simulation of my system,
for which the non-bonded interaction potential has the polarization term
as -Dij/(rij**4) in addition to the Bucking ham potential and
electrostatic interactions. So the non-bonded potential will appear as
Thee are not yet parameters for DDM but indeed the parameters for both
the head and the tail are defined separately. It would be very useful
to combine them and start building a detergent parameter library ...
the topologies would have to be tested against experimental and/or
atomistic da
Dear Gmx Users,
Which coarse grained force filed would you suggest for studying proteins in
GMX? I have heard that Martini is not the best for such a system e.g.
proteins interactions in water.
thanks,
Steven
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/li
The choice of CG force field is (as for atomistic) rather strongly
dependent on the problem your are looking at. Martini is far from
being perfect but it is really good at many things and proteins are
not so bad but don't expect folding (yet).
I am not aware of other CG FF adapted to GMX
This approach still requires the system to be parameterized as a single
moleculetype, doesn't it?
On 2012-05-20 04:42:26PM +0200, francesco oteri wrote:
> Hi,
> if you are able to define atom couples able to mantein the structure of
> your complex,
> you can insert in .top file a set of bond using
You are right Peter
2012/5/21 Peter C. Lai
> This approach still requires the system to be parameterized as a single
> moleculetype, doesn't it?
>
> On 2012-05-20 04:42:26PM +0200, francesco oteri wrote:
> > Hi,
> > if you are able to define atom couples able to mantein the structure of
> > your
Many thanks for your response
On Mon, May 21, 2012 at 12:01 PM, francesco oteri wrote:
> You are right Peter
>
> 2012/5/21 Peter C. Lai
>
> This approach still requires the system to be parameterized as a single
>> moleculetype, doesn't it?
>>
>> On 2012-05-20 04:42:26PM +0200, francesco oteri
Hi,
what is the easiest way to concatenate .log files? Is there a tool like
trjcat for trajectory files? Or do I have to do it by hand?
I recently had to restart a REMD simulation from checkpoint files after
it crashed. I did not use the append option and now have two log files
for each repl
On 5/20/12 2:30 AM, jrustad wrote:
Justin A. Lemkul wrote
You don't need the pull code if the two atoms are in the same
[moleculetype] - a
"molecule" in Gromacs is any set of atoms; they don't necessarily have to
make
chemical sense. The only problem I see is that if you have two atoms in
On 5/20/12 8:18 AM, delara aghaie wrote:
Dear Gromacs Users
I am doing Justin's Lysozyme tutorial. In EM step I got the error with molecule
type. (I am using Gromacs, 4.0.5)
It was about Cl and Na. I noticed that because I have selected OPLS forcefield,
I should change the name of Cl and Na in
On 5/21/12 7:47 AM, Ramya LN wrote:
Hello all,
I am doing protein-ligand dynamics using GROMACS. i could get all the final
files after simulation like gro,edr, log files. But i couldnt get the trr
file.Can anyone of you please tell me wht should i do to get this or tell me at
what step i have d
On 5/21/12 2:43 PM, Alan wrote:
Hi there,
Is there an option in pdb2gmx that when generating the top/itp file, it could
show the parameters explicitly? e.g.:
Instead of:
[ dihedrals ]
; aiajakal functc0c1c2
c3
5131112 4
On 5/21/12 7:25 PM, Andreas Zink wrote:
Hi,
what is the easiest way to concatenate .log files? Is there a tool like trjcat
for trajectory files? Or do I have to do it by hand?
I recently had to restart a REMD simulation from checkpoint files after it
crashed. I did not use the append option a
On 5/21/12 10:05 AM, Du Jiangfeng (BIOCH) wrote:
Please don't reply to the entire digest message; copy and paste only the
relevant parts.
On 5/16/12 4:08 AM, Du Jiangfeng (BIOCH) wrote:
Dear Sir/Madam,
I have performed umbrella pulling and umbrella sampling my protein from a
DOPC/DOPS mem
Hi.
I've been trying to build my system in gromacs and have run into a problem. On
my initial energy minimization after building the .go and .top files, I
inevitably get 1 atom that doesn't get below the specified fmax (fmax of 10 in
my case: the force on the atom is around 60-90). This remains
On 5/21/12 8:10 PM, patrick wintrode wrote:
Hi.
I've been trying to build my system in gromacs and have run into a problem. On
my initial energy minimization after building the .go and .top files, I
inevitably get 1 atom that doesn't get below the specified fmax (fmax of 10 in
my case: the for
21 maj 2012 kl. 06.54 skrev Anirban:
>
>
> On Mon, May 21, 2012 at 3:09 AM, mu xiaojia wrote:
> Thanks for prompt answering but I may need to clarify my question and sorry
> for the understanding,
>
> For example, I have dipeptides like Ala-Ala, how to ask g_hbond only
> calculate the h bon
Dear all gromacs users,
I tried the grompp and i got the following
error.
Fatal error:
number of coordinates in coordinate file (1UZ9_ion.gro, 41103)
does not match topology (1UZ9.top, 41100)
Is there any explanation why is thid happening?
I would
Hi Suryanarayana,
http://www.gromacs.org/Documentation/Errors is where i'd start. But to help
you along this error suggests that you have a different number of atoms in
your coordinate file(.gro) than your topology(.top) suggests. Often this can
be caused by adding or removing ions or solvent
Thank you Justin. But if i want to extend my simulation, i need trr file...
right?then how should i proceed?
On Mon, May 21, 2012 at 11:18 PM, Justin A. Lemkul wrote:
>
>
> On 5/21/12 7:47 AM, Ramya LN wrote:
>
>> Hello all,
>> I am doing protein-ligand dynamics using GROMACS. i could get all th
On 5/22/12 7:17 AM, Ramya LN wrote:
Thank you Justin. But if i want to extend my simulation, i need trr file...
right?then how should i proceed?
You do not need a .trr file to extend a simulation unless you are using an
ancient version of Gromacs. See the following:
http://www.gromacs.or
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