*Dear All,
After Installing gromacs, ngmx not seems to work and going
through the blogs I understood that it because of some X libraries. Could
anybody suggest how to install these libraries and make ngmx work.
Thank you*
*With Regards,
Ravi Kumar Venkatraman,
IPC Dept., IISc,
Install libx11-dev (in ubuntu) or something similar before you install
gromacs. It worked for me.
Luís
On 30 November 2011 08:55, Ravi Kumar Venkatraman
ravikumarvenkatra...@gmail.com wrote:
*Dear All,
After Installing gromacs, ngmx not seems to work and going
through the
Hey :)
I think I recall there was a way to suppress writing step*.pdb files,
but I couldn't find it. Anyone know from the top of his/her head?
Otherwise I'll go and check the source...
Oh, trust me... I know what I'm doing ;) Even though it's insane... :D
Groetjes,
Tsjerk
--
Tsjerk A.
dear teacher,
i want to modify the gromacs4.5.5 code ,can i use function cout which is
introuduce in c++.
i add the code
#include string.h
#include iostream
at the head of the md.c
but when i make , there is a error
md.c:103:20: error: iostream: No such file or directory
thanks
regards,
Bo Du
Use fprintf(stdout, …);
Carsten
On Nov 30, 2011, at 12:27 PM, 杜波 wrote:
dear teacher,
i want to modify the gromacs4.5.5 code ,can i use function cout which is
introuduce in c++.
i add the code
#include string.h
#include iostream
at the head of the md.c
but when i
On 30/11/2011 9:56 PM, Tsjerk Wassenaar wrote:
Hey :)
I think I recall there was a way to suppress writing step*.pdb files,
but I couldn't find it. Anyone know from the top of his/her head?
Otherwise I'll go and check the source...
Oh, trust me... I know what I'm doing ;) Even though it's
Mark Abraham wrote:
On 30/11/2011 9:56 PM, Tsjerk Wassenaar wrote:
Hey :)
I think I recall there was a way to suppress writing step*.pdb files,
but I couldn't find it. Anyone know from the top of his/her head?
Otherwise I'll go and check the source...
Oh, trust me... I know what I'm doing ;)
Thanks guys! I see I'm using an outdated manual...
Tsjerk
On Wed, Nov 30, 2011 at 1:28 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Mark Abraham wrote:
On 30/11/2011 9:56 PM, Tsjerk Wassenaar wrote:
Hey :)
I think I recall there was a way to suppress writing step*.pdb files,
but I
Hello,
Please let me know what is the unit of r (nm or A) in the radial
distribution function
output(rdf.xvg) of the program g_rdf in gromacs. As the output shows no units.
--
---
Regards,
Bipin Singh
--
gmx-users mailing listgmx-users@gromacs.org
Hi Bipin,
Gromacs uses nm.
Cheers,
Tsjerk
On Wed, Nov 30, 2011 at 3:32 PM, bipin singh bipinel...@gmail.com wrote:
Hello,
Please let me know what is the unit of r (nm or A) in the radial
distribution function
output(rdf.xvg) of the program g_rdf in gromacs. As the output shows no units.
Dear Prof.
I have a system consists of 10 micelle after production simulation. How can I
select a micelle with 92 monomer?
I know that I should use from g_select, but I don't know which argument is
proper for me. I also checked -select help in g_select program.
Please help me.
Best Regards
--
mohammad agha wrote:
Dear Prof.
I have a system consists of 10 micelle after production simulation. How
can I select a micelle with 92 monomer?
I know that I should use from g_select, but I don't know which argument
is proper for me. I also checked -select help in g_select program.
Please
Thanks.
On Wed, Nov 30, 2011 at 20:06, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Bipin,
Gromacs uses nm.
Cheers,
Tsjerk
On Wed, Nov 30, 2011 at 3:32 PM, bipin singh bipinel...@gmail.com wrote:
Hello,
Please let me know what is the unit of r (nm or A) in the radial
distribution
The Y-size of the box (1.999239) times the triclinic skew factor
(1.00) is smaller than the number of DD cells (2) times the
smallest allowed cell size (1.00)
I don't understand the fatal error message it has been given during a
simple run,
I tested with large box already, during
https://docs.google.com/open?id=0B93SVRfpVVg3NTVjMmY0NzEtM2UzOC00MDEwLWI2OWMtZjEyZDQ5NzM1YWVh
I uploaded the files here.
is it the box still small?
Thanks,
On Thu, Dec 1, 2011 at 12:25 AM, lina lina.lastn...@gmail.com wrote:
The Y-size of the box (1.999239) times the triclinic skew factor
Dear Experts,
Hi,
Is there any tools in gromacs to get Hydrophobic cores of protein ?
Best,
Hyun --
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Hello dear GMX Users,
Through scripting, I have an itp-like file to restrain all atoms that are NOT
within a 30 angstroms radius from the center (a trimmer + water + ions).
This selection includes both protein and solvent atoms, which may be a problem
when assigning this selection to the TOP
Hi Ricardo,
Unfortunately that is not possible. What you can do is rearrange the water
in the structure and use two water moleculetypes, one with and one without
position restraints. It might be nice to have something like
global_position_restraints, added under [ system ], but that needs to be
김현식 wrote:
Dear Experts,
Hi,
Is there any tools in gromacs to get Hydrophobic cores of protein ?
I suppose that depends on what your definition is, but in all likelihood no, not
directly. A program like g_sas can give you nonpolar and polar surface areas as
well as volumes and
Dear Gromacs users
Is there any script that does a PB or GB calculation to perform a
MM/PB(GB)SA free energy calculation in Gromacs. Similar to the MMPBSA.py
script available in Amber. I find a similar question raised by a user a
couple of years back. Any successful implementation
Hi!
There is support in gromacs for gb calculations. However, I'm currently
investigating some recent reports about unstable simulations (unfolding
proteins), so my advice is to use the code with caution.
Thanks
/Per
30 nov 2011 kl. 20:04 skrev R.S.K.Vijayan biovija...@gmail.com:
Dear
Hi,
I would like to run a gas-phase protein simulation (with charge state of +8).
I have read this paper : Biochemistry, 2007, 47, 933-945.
In the method section of vaccum simulation, it is said
For the remaining parameters, the same settings were used as in the water
simulations,
except that
mohammad agha wrote:
Thanks for your reply, but how can I define residue numbers of one
micelle from between 10 micelle that all of them are same and only were
differ at the number of monomer in micelle.
May I know how, please?
Well, now the problem is potentially more complicated. Two
yes all cutoffs 0 and epsilon_rf 1 and nstlist 0 as well.
Toodle pip!
On Nov 30, 2011, at 8:39 PM, Shi, Huilin huil...@imail.iu.edu wrote:
Hi,
I would like to run a gas-phase protein simulation (with charge state of
+8).
I have read this paper : Biochemistry, 2007, 47, 933-945.
In
Shi, Huilin wrote:
Hi,
I would like to run a gas-phase protein simulation (with charge state
of +8).
I have read this paper : Biochemistry, 2007, 47, 933-945.
In the method section of vaccum simulation, it is said
For the remaining parameters, the same settings were used as in the
water
Thanks for your reply.
Best Regards
From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Wednesday, November 30, 2011 11:27 PM
Subject: Re: [gmx-users] g_select
mohammad agha wrote:
Thanks for your
I am using a new cluster of Xeons and, to get the most efficient
compilation, I have compiled gromacs-4.5.4 separately with the intel,
pathscale, and pgi compilers.
With the pgi compiler, I am most concerned about this floating point
overflow warning:
...
[ 19%] Building C object
Hi,
Thank you for your reply.
My concern is that if rcoulomb and rvdw are set to be zero, does it mean that
there are no coulombic and van der waals forces involved in the simulation?
I guess there are still coulombic and van der waals forces between atoms of a
single protein molecule.
Or
Shi, Huilin wrote:
Hi,
Thank you for your reply.
My concern is that if rcoulomb and rvdw are set to be zero, does it
mean that
there are no coulombic and van der waals forces involved in the simulation?
I guess there are still coulombic and van der waals forces between atoms
of a single
Hi Gmxers,
I used g_dist to find all water molecules within 5 Angstrom of a protein in a
trajectory with a little surprise that gromacs directly prints out those water
on my screen rather than in an output file.
Since in each frame, those water molecules are not the same, I realize I need
to
Have you run g_energy on the .edr file and extracted the box dimensions during
the run to see what has been happening to them?
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
Dear gmx users:
I am using the free energy to calculate the ligand binding affinity to protein,
during the decouple process, I need to put some restraint between the protein
and the ligand, e.g. distance restraint.
But distance restraint is only for intramolecular, so I need to make a hybrid
Yao Yao wrote:
Hi Gmxers,
I used g_dist to find all water molecules within 5 Angstrom of a protein
in a trajectory with a little surprise that gromacs directly prints out
those water on my screen rather than in an output file.
According to g_dist -h, that's what you should expect :)
Chunxia Gao wrote:
Dear gmx users:
I am using the free energy to calculate the ligand binding affinity to protein,
during the decouple process, I need to put some restraint between the protein
and the ligand, e.g. distance restraint.
But distance restraint is only for intramolecular, so I
Dear gmx-users,
I want to make a long nano-fiber composed of many non-covalently bonded
proteins, it elongates along the Z axial direction.
in editconf, we can define the Distance between the solute and the box,
but it works for x,y and z directions at the same time.
e.g. my command
editconf -f
On 1/12/2011 10:24 AM, mu xiaojia wrote:
Dear gmx-users,
I want to make a long nano-fiber composed of many
non-covalently bonded proteins, it elongates along the Z axial direction.
in editconf, we can define the Distance between the solute and the
box, but it works for x,y and z directions
On 1/12/2011 3:25 AM, lina wrote:
The Y-size of the box (1.999239) times the triclinic skew factor
(1.00) is smaller than the number of DD cells (2) times the
smallest allowed cell size (1.00)
I don't understand the fatal error message it has been given during a
simple run,
I tested
mu xiaojia wrote:
Dear gmx-users,
I want to make a long nano-fiber composed of many non-covalently bonded
proteins, it elongates along the Z axial direction.
in editconf, we can define the Distance between the solute and the
box, but it works for x,y and z directions at the same time.
Hi Justin,
Thanks for your hints. I feel the string in g_select is pretty much like tck/tl
in VMD.
However I have not figured out the way to select a customized group defined in
.ndx file.
And one more question I have, maybe more general, if I have, say, 100 frames,
g_select will give me
Yao Yao wrote:
Hi Justin,
Thanks for your hints. I feel the string in g_select is pretty much like
tck/tl in VMD.
However I have not figured out the way to select a customized group
defined in .ndx file.
There's one example in the help text that is almost exactly what you want, is it
On Thu, Dec 1, 2011 at 7:45 AM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 1/12/2011 3:25 AM, lina wrote:
The Y-size of the box (1.999239) times the triclinic skew factor
(1.00) is smaller than the number of DD cells (2) times the
smallest allowed cell size (1.00)
I don't
Now I used mdrun -nt 2
it showed:
Fatal error:
One of the box vectors has become shorter than twice the cut-off
length or box_yy-|box_zy| or box_zz has become smaller than the
cut-off.
and mdrun -nt 1 it showed:
Program mdrun, VERSION 4.5.4-dev-20110711-dadcb
Source code file:
Dear Sir,
I am studying a protein complex. I have perforemed 10ns simulations. I
saved snapshots every10ps. sp all snap shopts I got were 1000.
Now I want to analyse them with respect to interactions. I want to check
the binding surfaces and binding points which come closer and incontact
during
Hi Saba,
You can use g_mdmat or run g_rmsdist for different time windows.
It's also a good idea to have a look at all the analysis tools and
think of how they may suit your purpose.
Cheers,
Tsjerk
On Thu, Dec 1, 2011 at 5:43 AM, Saba Ferdous saba.bsbi...@iiu.edu.pk wrote:
Dear Sir,
I am
Dear GMX users,
I could make topology file of a ligand molecule by PRODRG but it has wrong
charge on each atom and as mentioned in Gromacs tutorial (protein-ligand
complex) I have used quantum mechanic calculation (like spartan) to correct
its charge:
.itp file from PRODRG:
[ atoms ]
; nr
Hi,
Hi,
I have done a simulation of 10ns with my proteins and 0.5 M phosphate ion.
Now I want to know where does the phosphate ion bind on the protein surface
or distribution of phosphate ions on protein surface ?? .. can help me
finding out this
Regards
--
Bharat
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