Hi,
I have successfully converted my CG (only) protein model to FG model using
g_fg2cg command of the gromacs_reverse package. But now when I try to
compile my .mdp file for SA run, grompp is throwing some warnings:
creating statusfile for 1 node...
Back Off! I just backed up mdout.mdp to
Dear all
I have been using g_hbond of gromacs4.0.7 and 4.5.3 both gives me different
results. is there any updates in the hbond tool
E R Azhagiya singam
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babu gokul skrev 2011-02-14 11.28:
Dear all
I have been using g_hbond of gromacs4.0.7 and 4.5.3 both gives me
different results. is there any updates in the hbond tool
E R Azhagiya singam
This has been reported but not fixed as far as I know. Embarresingly I'm
probably the one who shoud fix
Anirban Ghosh wrote:
Hi,
I have successfully converted my CG (only) protein model to FG model
using g_fg2cg command of the gromacs_reverse package. But now when I try
to compile my .mdp file for SA run, grompp is throwing some warnings:
creating statusfile for 1 node...
Back Off! I just
Dear Gromacs users and developers,
I'm interested to run simulation of natively unstructured protein
(casein), that can self assembly and create micelles, using Martini
force field. The initial structure of the monomer was created and
minimized using Sybyl. This protein includes also 4
Dear Regina,
You have two problems:
1- the parameterization of phosphorylated serine should be done
following the same philosophy of Martini. Check the Martini papers
to see how this is done. In short partitioning is of primary importance.
2- you want to simulate unfolded protein ... indeed
Dear all,
I know there are sections about virtual sites usage in gromacs manual. But
it is somehow unclear for me to use. So I would like to ask how to use
virtual sites in my input file. I have follow the the example from
tip4p.itp and write my own virtual site is *.itp as:
[ atoms ]
; nr
Dear gmx-users,
I have a system formed by protein+ligand+lipid bilayer that accounts for
about 10500 residues (56000 atoms). It seems to me that it is not possible
to visualize correctly such a large system with Pymol or VMD, because it
seems that the max number of residues that I can manage with
Hi Anna,
The 'problem' is the PDB file format. It is a fixed-width format that
does not allow for residue numbers with more than 4 digits. Both VMD
and PyMOL do not have problems reading structures with more residues,
but they will choke if you renumber the residues, giving numbers with
five or
Hi Justin,
As discussed earlier, I removed the restraints from lipids and used constraint
force for pulling, I was able to pull the peptide to the lower leaf headgroups
starting from 1.3nm above the upper leaf headgroups. Below is the pull code
inputs i used:
; Pull code
pull=
Dear Tsjerk,
thank you very much. I really didn't know that the PDB format does not allow
more than residues (in fact, it is the first time I have such a big
system to manage). I will follow your suggestions trying to solve the
problem with chain identifiers.
Many thanks and best regards
Anna
Poojari, Chetan wrote:
Hi Justin,
As discussed earlier, I removed the restraints from lipids and used constraint
force for pulling, I was able to pull the peptide to the lower leaf headgroups
starting from 1.3nm above the upper leaf headgroups. Below is the pull code
inputs i used:
; Pull
Hi Anna,
I didn't say the PDB format does not allow more than residues. It
does. But it does not allow numbers higher than . Thus, with more
residues, it will start counting over.
Cheers,
Tsjerk
On Mon, Feb 14, 2011 at 4:52 PM, Anna Marabotti
anna.marabo...@isa.cnr.it wrote:
Dear
hi all,
i want to perform stochastic dynamics (sd) simulations in implicit
mesitylene. and first i wanted to understand how the value of the
friction coefficient for water sd simulations is chosen.
gromacs manual suggests a value of 0.5 1/ps (which is lower then the
internal friction of
On 14/02/11 13:42, XAvier Periole wrote:
Dear Regina,
You have two problems:
1- the parameterization of phosphorylated serine should be done
following the same philosophy of Martini. Check the Martini papers
to see how this is done. In short partitioning is of primary importance.
2- you want
Hello Anna,
If you just need to vizualize the PDB file, you can code the residue Id in
hexadecimal and vizualize it with VMD. VMD is able to read hex number in
PDB files.
Cheers,
Nicolas
Hi Anna,
The 'problem' is the PDB file format. It is a fixed-width format that
does not allow for
Dear All,
I am trying to install gromacs in ubuntu. I configured both fftw and gromacs in
my home folder following the instructions on
http://www.gromacs.org/Downloads/Installation_Instructions. However, when I do
make, I get an error in the end (pasted below). I have also attached the log
Thank you very much for you reply. Can you please explain me why do i
need secondary structure file at all and why secondary structure is
pre-defined and thus static throughout a simulation? I didn't see
that something like this defined for lipids. How do I use do_dssp to
build the needed
Dear experts,
I am going to do solvation FE of polymer (polyethylene) in a hydrocarbon
solvent. I have prepared a system consisting of 4 polymer chains and 480
hexane molecules with the actual density of polymer solution (~ 0.5 g/cm3).
1- For such a study I dont know how many polymers I need to
How close are the polymers in space?
On February 14, 2011 at 3:28 PM Moeed lecie...@googlemail.com wrote:
Dear experts,
I am going to do solvation FE of polymer (polyethylene) in a hydrocarbon solvent. I have
On February 14, 2011 at 3:28 PM Moeed lecie...@googlemail.com wrote:
Dear experts,
I am going to do solvation FE of polymer (polyethylene) in a hydrocarbon solvent. I have prepared a system consisting of 4
1. Seems the default fftw configuration is double,
when you install the fftw-3.2.2 configure with --enable single.
2. about your question:I wanted to ask if I can download gromacs in my home
directory using the ubuntu software center or synaptic manager?
1] You can download in your home
Okay, I'll try with --enable-single. But as far as I understood, it seems like
its an issue with --enable-shared. In the first attempt, I did enable-shared in
fftw configuration, but didn't do it in gromacs configuration, and got this
error. In the second attempt, I did enable-shared in
majid hasan wrote:
Okay, I'll try with --enable-single. But as far as I understood, it
seems like its an issue with --enable-shared. In the first attempt, I
did enable-shared in fftw configuration, but didn't do it in gromacs
configuration, and got this error. In the second attempt, I did
Okay, thanks, I'll look into config.log. Can you tell me about this
error: relocation R_X86_64_32 against `.rodata' can not be used when making
a shared object; recompile with -fPIC. Does it have something to do with
--enable-shared during configuration of fftw, and gromacs?
Best Regards,
You are right, it's relevant to the shared libs.
but I don't know why you failed in the second attempt if you did a clean
reinstallation.
lina
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Okay. Actually, second time, I over-worte the first installation. I mean I
didn't uninstall the first one, I just ran the whole process again starting
from
fftw$./configure. I am not sure if that is all right, I just did it to find out
the problem. In the third attempt (without issuing
clean reinstallation.
make uninstall
make distclean
rm -r the untar one
from source re-install it again.
lina
On Tue, Feb 15, 2011 at 12:39 PM, majid hasan pu_majidha...@yahoo.comwrote:
Okay. Actually, second time, I over-worte the first installation. I mean I
didn't uninstall the first
Okay, I'll do this. I have also realized after browsing through config.log,
that
Xlib.h is absent. Where do I get it, I want it to run ngmx.
Thanks,
Majid
From: ZHAO Lina lnzha...@gmail.com
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent:
On 15/02/2011 4:35 PM, majid hasan wrote:
Okay, I'll do this. I have also realized after browsing through
config.log, that Xlib.h is absent. Where do I get it, I want it to run
ngmx.
You will need the X windowing system installed, and probably the
associated devel packages. Use your
On Feb 14, 2011, at 7:24 PM, devicerandom wrote:
On 14/02/11 13:42, XAvier Periole wrote:
Dear Regina,
You have two problems:
1- the parameterization of phosphorylated serine should be done
following the same philosophy of Martini. Check the Martini papers
to see how this is done. In short
On Feb 14, 2011, at 11:43 PM, pol...@fh.huji.ac.il wrote:
Thank you very much for you reply. Can you please explain me why do
i need secondary structure file at all and why secondary structure
is pre-defined and thus static throughout a simulation? I didn't
see that something like this
Hi Regina,
Most CG force fields for proteins are less versatile than all-atom force fields
and are simply not adequate for every application. As the secondary structure
is determined a priori, you cannot model secondary structure changes, as
probably happen during aggregation - even if the
Dear Erik
which version of g_hbond is correct so that i ll use that for my analysis
E R Azhagiya singam
From: Erik Marklund er...@xray.bmc.uu.se
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc: babu gokul bb...@yahoo.co.in
Sent: Mon, 14
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