Hi all
I want to generate a contact map for all the residues of lysozyme protein.
I am using gmx mdmat to generate this. Can I generate a text file (which
can be open in Grace) except the image files(eg: xpm file)? Please let me
know the particular flag which I can use to get a *.xvg file.
Thanks
I was looking for DPD in Gromacs too but in vain. You may try DPDmacs, POLY DL
or LAMPPS.
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Forgot to mention Materials Studio. An extremely easy-to-use software but
comes at a hefty license fee.
On Oct 24, 2017 5:57 PM, Raman Preet Singh
mailto:ramanpreetsi...@hotmail.com>> wrote:
I was looking for DPD in Gromacs too but in vain. You may try DPDmacs, POLY DL
or LAMPPS.
--
Groma
Friend,
I may have some older version of DPD-gromacs. However, I am not sure for
what you need it. Being trial, that version might not be completely free of
errors.
Nicu
On Tue, Oct 24, 2017 at 3:27 PM, Raman Preet Singh <
ramanpreetsi...@hotmail.com> wrote:
> I was looking for DPD in Gromacs t
Dear all, I want to use GMX to simulate ethanol solution
interaction with macromolecular in a polarizable force filed. Whether the
macromolecular and ethanol PDB files need adding Drude particles? and how to
produce an ethanol.itp file for Drude2013 force field? Do the Drude2013 for
On 10/24/17 12:08 AM, limingru wrote:
Hello Justin, Many thanks for your answer. Another question
is that whether I need adding some Drude particles in my PDB file of DNA or
Protein in the simulation process, if any, how to modify the PDB file? I
pdb2gmx will build everyt
On 10/24/17 7:58 AM, sp...@iacs.res.in wrote:
Hi all
I want to generate a contact map for all the residues of lysozyme
protein.
I am using gmx mdmat to generate this. Can I generate a text file (which
can be open in Grace) except the image files(eg: xpm file)? Please let me
know the particula
Dear all, I want to use GMX to simulate ethanol molecules
interaction with macromolecular in a polarizable force filed. Whether the
macromolecular and ethanol PDB files need adding Drude particles, if any, how
to do? In addition, how to produce an ethanol.itp file for Drude2013 forc
Hello again,
Thank you very much for your answers, we got to convert everything. We used
pdb2gmx with no problems, and the conf.gro file looks fine (on VMD at
least). Then, we tried with a simple input file (from
http://www.gromacs.org/@api/deki/files/198/=gmx-tutorial.pdf), but grompp
reports a f
Hi,
I created a table for my own potential which has a 'constant' value. I
added it to the g(r) or h(r) functions in the table, but it gives incorrect
results.
I also can not shift the potential after simulation, since the x>cut-off
will be also shifted.
Any suggestion?
Best regards
--
Gromacs
Hello,
I want to create a topology file for ammonia molecule and run using oplsaa
FF. since ammonia molecule is not there in oplsaa FF, i created the
molecule in Avogadro software and saved it as .pdb format. Then using the
topolgen_1.1.pl pearl script (script by Justin Lemkul), i generated the
top
On 10/24/17 1:11 PM, Dilip H N wrote:
Hello,
I want to create a topology file for ammonia molecule and run using oplsaa
FF. since ammonia molecule is not there in oplsaa FF, i created the
molecule in Avogadro software and saved it as .pdb format. Then using the
topolgen_1.1.pl pearl script (scr
Solved!!
the constant can be added to the table, to g(r) or h(r).
Best regards
On Tue, Oct 24, 2017 at 7:05 PM, Faezeh Pousaneh
wrote:
> Hi,
>
> I created a table for my own potential which has a 'constant' value. I
> added it to the g(r) or h(r) functions in the table, but it gives incorrec
Hi Everyone,
Like to know your thoughts on this.
I appreciate any comment on this in advance.
Cheers,
Mohsen
On Wed, Oct 18, 2017 at 7:26 PM, Mohsen Ramezanpour <
ramezanpour.moh...@gmail.com> wrote:
> Hi Justin, Tom, Antonio,
>
> I read the articles recommended in the previous emails.
> To get
Hello Elisa,
"J'arrive après la bataille" To be sure that you have correct Amber parameters
for GROMACS, you could also use the acpype suite*. This suite converts Amber
params in gromacs format. The program generates the (non)ffbonded.itp and top
files in gromacs format from the Amber's LeaP
Please, get it here
svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/
stable/ccpn/python/acpype acpype
Interestingly, but Google code still holds the correct information too:
https://code.google.com/archive/p/acpype/
On 24 October 2017 at 18:34, ABEL Stephane wrote:
> Hello
Dear GROMACS users
I need to work on a cluster which has 30 nodes, each has 8 processors
I need to work on 8 nodes (64 processors). For mdrun I used this command:
mpirun -np 64 gmx_mpi mdrun ..
but the simulation failed to start and here is the error
--
Hi,
This is a general issue with using MPI programs, not one specific to
GROMACS. Please read and follow the instructions for your cluster. The MPI
system needs to know how to find gmx_mpi on each rank on each node, but how
you should do this depends whether there's modules in use, or you have to
> There's several dozen lines of performance analysis at the end of the log
> file, which you need to inspect and compare if you want to start to
> understand what is going on :-)
Thank you for the feedback. Fair warning, I'm more of a system administrator
than a regular gromacs user. What is
Thanks alot Goga N and Raman Preet Singh,
I have to simulate the polymer thin film of the order of sub nanometer
length scale, though I have gone through the DPDMacs, am able to run simple
DPD calculations, but haven't found any reference article that used
DPD-MACS. In addition to that we cannot s
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