In short - you can apply PBC in all directions (XYZ) by choosing the proper
keyword in the .mdp file, I believe the box dimensions are defined in .gro
file.
Omer.
Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
On Fri, Oct 10, 2008 at 16:
Hello, all! I intend to simulate a protein confined in a box. Can anybody
tell me how to define a boundary, or a wall, in GROMACS? Thanks!
--
Sun Li
Department of Physics
Nanjing University, China
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The topologies should not be identical, surely? Check out the section on
improper dihedrals in the manual, it's possible to specify an improper to keep
enantiomers in their intended handedness.
- Original Message
From: Anthony Costa <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent
Anthony Costa wrote:
i have a simulation where i would like to study the interaction of N
small molecules of various enantiomeric composition.
if i use a simple R+S situation (N=2) by inserting the other
enantiomer into my already created box, subsequent minimization either
yields unphysical s
i have a simulation where i would like to study the interaction of N
small molecules of various enantiomeric composition.
if i use a simple R+S situation (N=2) by inserting the other
enantiomer into my already created box, subsequent minimization either
yields unphysical structures for the inserte
Hi, all,
In a previous email, I asked about the availability of implicit water
calculations in Gromacs 4.0, which might be available in Gromacs 4.1.
In the meantime, I was wondering if I position restrained waters that
are 6 Angstroms from the protein, would that increase the speed of md
You might want to try Simbody (simtk.org). This will allow you to
rigidify any part or parts of the molecule you choose. As a bonus,
you will not spend resources computing intramolecular interactions in
the rigidified regions.
Sam
On Oct 10, 2008, at 6:10 AM, Justin A. Lemkul wrote:
Sorry for the trivial question, but I am new in Gromacs. I try to simulate a
polystyrene film and I want to use a 8.pdb file from an equilibrated film of
32 chains, 80 monomers each. I unterstand that I should enter the residues
(for the first, inner and last monomer(s)) and maybe to define the cor
Maybe I didn't put it clearly. My intention is to simulate a protein
confined in a box, and the problem is that I don't know how to define a
boundary, or a wall, in GROMACS.
2008/10/10 Omer Markovitch <[EMAIL PROTECTED]>
> Boundary should not "precisely" be around the protein, otherwise some part
Hi,
On Friday, 10. October 2008, andrea spitaleri wrote:
> Hi there,
> have look to "corina" software. I dont think it is free.
> http://cheminf.cmbi.ru.nl/cheminf/corina/
corina is a commerical product see
http://www.molecular-networks.com/software/corina/
You can try cdk it should convert 2d
vivek sharma wrote:
Hi justin,
My apologies for asking you so many small queries.
Can you suggest any good tutorial or reference that talks about this
issue of running MD over a selected part of molecule.
If you're using PR, all you're doing is position-restrained dynamics.
-Justin
With
vivek sharma wrote:
hI justin,
Thanks for your response.
do I need to specify the index file(for residue that I want to keep fix
during MD) during GROMPP or just including the psre.itp in topology is
enough for the purpose ?
No; you just need it to pass to genpr.
Please remember to copy t
Use the PRODRG server; it is free:
http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta
-Justin
andrea spitaleri wrote:
Hi there,
have look to "corina" software. I dont think it is free.
http://cheminf.cmbi.ru.nl/cheminf/corina/
and
vivek sharma wrote:
Hi there,
Is there any open source p
Hi justin,
My apologies for asking you so many small queries.
Can you suggest any good tutorial or reference that talks about this issue
of running MD over a selected part of molecule.
With Thanks,
Vivek
2008/10/10 vivek sharma <[EMAIL PROTECTED]>
> hI justin,
>
> Thanks for your response.
> do
Hi there,
have look to "corina" software. I dont think it is free.
http://cheminf.cmbi.ru.nl/cheminf/corina/
and
vivek sharma wrote:
Hi there,
Is there any open source package to convert 2-D structure of a molecule to
3-D structure ?
If anybody have tried such thing, please suggest me te way
hI justin,
Thanks for your response.
do I need to specify the index file(for residue that I want to keep fix
during MD) during GROMPP or just including the psre.itp in topology is
enough for the purpose ?
With Thanks,
Vivek
2008/10/10 Justin A. Lemkul <[EMAIL PROTECTED]>
>
>
> Justin A. Lemkul
Hi there,
Is there any open source package to convert 2-D structure of a molecule to
3-D structure ?
If anybody have tried such thing, please suggest me te way to do the same.
I am having openbabel on my system, does openbabel i shaving such
functionality ?
please suggest ?
With thanks,
Vivek
Justin A. Lemkul wrote:
vivek sharma wrote:
Thanks Justin,
My goal is to keep certain part fixed and move only a few of the
residues (case is like providing flexibility to the site of interest
only).
SO , do I need to specify the residue using some index file ?
or is there some other wa
Thanks Justin,
My goal is to keep certain part fixed and move only a few of the residues
(case is like providing flexibility to the site of interest only).
SO , do I need to specify the residue using some index file ?
or is there some other way to specify the part of molecule for position
restrai
vivek sharma wrote:
Hi there,
I want to run MD over a part of my molecule , for few residues only (not
the whole molecule).
Can I do it using GROMACS ?
I searched for the online documentation and mailing list, but unable to
get appropriate information.
If somebody has already tried such th
vivek sharma wrote:
Hi There,
I am running a long MDS for one protein molecule in water, To avoid
error I am running the simulation in parts like 20 nsec each.
Each time I am creating a new tpr, trr and edr using the tpbconv and mdrun.
Last time when I fired a job for 60-80 nsec then the job
Kwee Hong wrote:
Hi.
I'm very new to iMAC as I've just started to use it for about one month.
I would like to install GROMACS on it but i seem can't find any
step-to-step installation instruction. All those that I found was seem
to be instruction for linux. Can you give me some idea on how
I have created a wiki entry on this:
http://wiki.gromacs.org/index.php/compiling_QMMM
Gerrit
--
Gerrit Groenhof
MPI biophysical chemistry
Goettingen
Germany
http://www.mpibpc.mpg.de/groups/grubmueller/start/people/ggroenh/index.html
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gmx-users
Hi there,
I want to run MD over a part of my molecule , for few residues only (not the
whole molecule).
Can I do it using GROMACS ?
I searched for the online documentation and mailing list, but unable to get
appropriate information.
If somebody has already tried such things earlier, please suggest
Boundary should not "precisely" be around the protein, otherwise some parts
of the protein would "feel" other parts via the boundary.
In general, if you apply periodic boundary conditions (PBC), take the
dimensions as such so the protein would NOT feel the PBC.
Say you have an unfolded protein (or
But the problem is: how to define a boundary?
2008/10/10 Xavier Periole <[EMAIL PROTECTED]>
> On Fri, 10 Oct 2008 15:09:31 +0800
> "Lee Soin" <[EMAIL PROTECTED]> wrote:
>
>> Hi! I'm going to simulate a protein confined in a box. Can GROMACS do
>> this?
>> Will the removal of the periodic boundar
On Fri, 10 Oct 2008 15:09:31 +0800
"Lee Soin" <[EMAIL PROTECTED]> wrote:
Hi! I'm going to simulate a protein confined in a box. Can GROMACS do this?
Will the removal of the periodic boundary condition be OK?
The removal of the periodic boundary conditions will be equivalent to an
infinite box.
Hi! I'm going to simulate a protein confined in a box. Can GROMACS do this?
Will the removal of the periodic boundary condition be OK?
--
Sun Li
Department of Physics
Nanjing University, China
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