Respected sir,
I am studying about micelle formation .. After setting box and adding
water i went for energy minimization and then went for nvt equilibration
for 1ns. when i visualized my nvt.pdb file, i found that my protein comes
together and formed three micelle like structure. but my box
On 16/05/2012 4:18 PM, priya thiyagarajan wrote:
Respected sir,
I am studying about micelle formation .. After setting box and adding
water i went for energy minimization and then went for nvt
equilibration for 1ns. when i visualized my nvt.pdb file, i found that
my protein comes together
Hi Priya,
My query is different than your problem ..
I wondered Is you use position restrained in nvt...??
In position restrained protein comes togather or you remove
position restraind ...
Sorry for trouble you...
With Best wishes,
Rama David
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gmx-users mailing list
On 16/05/2012 1:50 AM, daviddesancho wrote:
Thanks Florian and Mark for your replies.
I have run the simulation for longer (one order of magnitude longer, i.e. 1
ns) and what I get now is that the 'conserved energy' follows its drift
linearly. Now, of course, we are speaking about 1.2% drift/ns
Dear all,
How to install DSSP in Gromacs 4.5.5.
i set environmental variable export DSSP=/usr/local/bin/dssp and checked.
I have refereed many posts related to dssp issue and tried with new and old
dssp executable but confused.
While running i got error Segmentation fault.
Help me to solve
On 16/05/2012 4:54 PM, Sathish wrote:
Dear all,
How to install DSSP in Gromacs 4.5.5.
i set environmental variable export DSSP=/usr/local/bin/dssp and
checked.
I have refereed many posts related to dssp issue and tried with new
and old dssp executable but confused.
While running i got
Gromacs version is 4.5.5 and mdp file is that from Justin's tutorial, step 6
(http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/nvt.mdp)
Thanks
-David
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View this message in context:
Dear Sir,
Thank u for reply and the old dssp executable was working fine,
[root@localhost]# dssp
COPYRIGHT
W. Kabsch, C. Sander and MPI-MF, 1983, 1985, 1988, 1994 1995
CMBI version by elmar.krie...@cmbi.ru.nl / April 1, 2010
USAGE
dssp [Options] PDB_File DSSP_File - Read PDB_File
On 16/05/2012 5:33 PM, Sathish wrote:
Dear Sir,
Thank u for reply and the old dssp executable was working fine,
[root@localhost]# dssp
COPYRIGHT
W. Kabsch, C. Sander and MPI-MF, 1983, 1985, 1988, 1994 1995
CMBI version by elmar.krie...@cmbi.ru.nl
mailto:elmar.krie...@cmbi.ru.nl
Hi
If I use pdb2gmx -f mymol.pdb -water tip3p (CHARMM27 force field) I got
warnings like this:
Making bonds...
Warning: Long Bond (1-2 = 0.261872 nm)
Warning: Long Bond (2-4 = 0.267812 nm)
Warning: Long Bond (6-4 = 0.260531 nm)
and so on
For what problem tries GROMACS to warn me? Should
On 16/05/2012 5:50 PM, Lara Bunte wrote:
Hi
If I use pdb2gmx -f mymol.pdb -water tip3p (CHARMM27 force field) I got
warnings like this:
Making bonds...
Warning: Long Bond (1-2 = 0.261872 nm)
Warning: Long Bond (2-4 = 0.267812 nm)
Warning: Long Bond (6-4 = 0.260531 nm)
and so on
For
Hi
After:
pdb2gmx -f mymol.pdb -water tip3p
editconf -f conf.gro -bt dodecahedron -d 1.3 -o box.gro
genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
I typed:
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
where em.mdp is my energy minimization file and I got:
Dear Sir/Madam,
I have performed umbrella pulling and umbrella sampling my protein from a
DOPC/DOPS membrane. Unfortunately, the results are really bad (Energy curve
suddenly turns to zero at the last 1 nm) and the histograph does not show any
overlap. Actually, I did it strictly based on
Thank you very much! I just saw your response.
As I run it in NPT ensemble the plot with volume is important for me.
Please, See the plot:
http://speedy.sh/CJn5b/tpiN.jpg
So does the fluctuating red curve make any sesnse then if it does not
consider volume?
Another thing: this is chemical
About the red curve, I guess fluctuations might be directly related to
volume fluctuations, you can extract the volume over time from g_energy
(boxXX*boxYY**boxZZ) and compare. (just another comment, now I am not
very sure about the f. that precedes the red line legend..)
About the
On Tue, 2012-05-15 at 19:47 +0100, Lara Bunte wrote:
Hello
To make better energy minimization procedures I read about thermostats and
barostats. I understand the physical concepts and differences between global
and local thermostats and the difference between Berendsen and Nose-Hoover
On Wed, May 16, 2012 at 10:28 AM, Javier Cerezo j...@um.es wrote:
About the red curve, I guess fluctuations might be directly related to
volume fluctuations, you can extract the volume over time from g_energy
(boxXX*boxYY**boxZZ) and compare. (just another comment, now I am not very
sure
Dear users,
I am doing Protein Ligand simulation, increasing temp. from 100, 200, to 300 K.
after 1ns of simulation in 300 K, the protein jumps out of the box and when I
use the command
trjconv_mpi -f *.trr -s *.tpr -o *new.trr -pbc nojump
followed by
trjconv_mpi -f new*.trr -s
Dear Gmx Users,
I would like to run energy minimization with some atoms restrained - this
is a surface made of atoms which do not share any bonds. So the EM of water
only. I tries to use define = -DPOSRES
in my EM file but then the surface atoms change their positions. Thus, when
I want to run
Hello Friends
I have installed GROMACS 4.5.5 on linux.
I put the DSSP Executable in /usr/local/bin
when i run the following command:
do_dssp -s md.tpr -f md.trr -b 40 -e 50 -o fws_ss.xpm
i got the following error.
Reading file md.tpr, VERSION 4.5.5 (single precision)
Reading file md.tpr, VERSION
Hi Florian,
Hi, there has been recently a discussion about this topic on this
mailing list. Check the archives for the information you look for.
However, Berendsen is not producing any kind of known ensemble, and
therefore only applicable for equilibration.
That's a very strong statement,
Hi Sogol,
You remove jumps over periodic boundary conditions, giving a
continuous trajectory. That gives you a very nice view on diffusion in
your system, which happens to be equal in all directions. Hence, the
end result looks spherical. But that's not the same as having a
spherical box. If you
Hi
Well, according to the link you pointed out, the Widom technique gives
you the excess chemical potential, as we discussed. mu and mu_ideal (in
your link) are not calculated, those are just the reference states
between which the Widom technique calculates the excess chem pot.
As I said, I
On 5/16/12 12:36 AM, rama david wrote:
On Tue, May 15, 2012 at 10:24 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
The parameters are missing from ffbonded.itp, making the implementation
incomplete. You can obtain a TFE topology from ATB:
On 5/16/12 1:01 AM, Anirban wrote:
Hi ALL,
I am simulating a membrane protein docked with a ligand and embedded in a lipid
bilayer. For COM removal I am using two groups, Prt_Lig_Lipid and SOL_CL.
For temperature and pressure couplings should I use these two groups or should I
use three
Hi Tsjerk,
sorry for the strong statement. I should have said:
should be applied ...
instead of
only applicable.
You are right, the question is how big is the difference and actually
one would also expect, that the differences vanish with 1/N. However, so
far it is unknown, what kind of
Dear All,
Will you please tell me how GROMACS calculates the total charge of a protein at
pH 6.5? And how do we assign the ionization state of the residues, especially
for HIS at pH 6.5?
I am looking forward to getting a reply from you.
Cheers,
Acoot--
gmx-users mailing list
On 5/16/12 5:57 AM, bunty xy wrote:
Hello Friends
I have installed GROMACS 4.5.5 on linux.
I put the DSSP Executable in /usr/local/bin
when i run the following command:
do_dssp -s md.tpr -f md.trr -b 40 -e 50 -o fws_ss.xpm
i got the following error.
Reading file md.tpr, VERSION 4.5.5 (single
On 5/16/12 5:54 AM, Steven Neumann wrote:
Dear Gmx Users,
I would like to run energy minimization with some atoms restrained - this is a
surface made of atoms which do not share any bonds. So the EM of water only. I
tries to use define = -DPOSRES
in my EM file but then the surface atoms
On 5/16/12 7:13 AM, Acoot Brett wrote:
Dear All,
Will you please tell me how GROMACS calculates the total charge of a protein at
pH 6.5? And how do we assign the ionization state of the residues, especially
for HIS at pH 6.5?
Gromacs does not automatically deal with anything aside from pH 7
On 5/16/12 3:56 AM, Lara Bunte wrote:
Hi
After:
pdb2gmx -f mymol.pdb -water tip3p
editconf -f conf.gro -bt dodecahedron -d 1.3 -o box.gro
genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
I typed:
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
where em.mdp is my
Hi
in my .rtp file I wrote in the [ atoms ] block
C2 CN1A 0.7481 1
but in the atomtypes.atp file I wrote
CN1A 12.01100
So I declared it. So what do you mean with such an atom type doesn't exist?
Greetings
Lara
- Ursprüngliche Message -
Von: Justin A. Lemkul
On 5/16/12 8:05 AM, Lara Bunte wrote:
Hi
in my .rtp file I wrote in the [ atoms ] block
C2 CN1A0.7481 1
but in the atomtypes.atp file I wrote
CN1A12.01100
So I declared it. So what do you mean with such an atom type doesn't exist?
Neither of those actions constitutes
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 membrane. Unfortunately, the results are really bad (Energy curve
suddenly turns to zero at the last 1 nm) and the histograph does not show any
Hi Gromacs Friends,
I plan to simulate protein In Trifluoro Ethanol solvent
using G96 53a6 FF
Please help to define parameters in md.mdp
For water I am using following mdp file
lincs_order= 4; also related to accuracy
; Neighborsearching
ns_type= grid; search
On 5/16/12 8:49 AM, rama david wrote:
Hi Gromacs Friends,
I plan to simulate protein In Trifluoro Ethanol solvent
using G96 53a6 FF
Please help to define parameters in md.mdp
For water I am using following mdp file
lincs_order= 4; also related to accuracy
;
Dear gmx users,
Which force fields are suggested for lipids? Except CHARMM, any other
forcefields?
Anybody may suggest me articles in this about?
Thanks in advance
Sincerely,
Shima--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please
Off the top of my head:
There are the Berger lipids for the gromos FFs (Justin's tutorial)
There was a B2 Adrenergic receptor paper that used Amber.
and of course Martini appears to be everyone's favorite coarse grain FF.
The literature search shall be left as an exercise for the reader.
(You can
One thought from justins post in the past,
Look at the .trj in VMD with the unit cell box and see if something sticks out
at the end (ie comes up in the bootmn of the box from the top). It then does
what you show, however it may not be that. If it is, you'll have to increase
your box
On 5/16/12 9:06 AM, Peter C. Lai wrote:
Off the top of my head:
There are the Berger lipids for the gromos FFs (Justin's tutorial)
There was a B2 Adrenergic receptor paper that used Amber.
and of course Martini appears to be everyone's favorite coarse grain FF.
There is also an OPLS-AA
Hi,
In addition to the ones already mentioned (CHARMM, GAFF/AMBER, Berger,
OPLS-AA) there are several united-atom GROMOS based lipid forcefields
(43A1-S3, 53A6L/54A7, 53A6 Kukol, etc.). The Lipidbook website is a
useful place to find lots of lipid parameters in one location:
Thanks for all your suggestions.
Honestly, I want to simulate a protein-membrane system. My chosen membrane is
POPC. After the simulation of the system, I'm gonna apply the umbrella sampling
on the system to study the ion conduction through the channel composed of this
protein.
Before this, I
Hi all,
I have learned from manual that non bonded interactions can be
given as user defined potential by using tables. If i want to give dihedral
term as user defined potential keeping rest of the bonded parameters in
their usual form, how can i do that.
Please suggest me a way,
On 5/16/12 10:25 AM, Steven Neumann wrote:
Dear Justin,
I pulled my ligad away of 6nm from the protein and obtained beautiful and smooth
curve of PMF using 28 windows. Starting from zero kcal/mol corresponding to app
0.3 nm then minima and curve increase till my plateau which starts from app
On 5/16/12 10:34 AM, mohan maruthi sena wrote:
Hi all,
I have learned from manual that non bonded interactions can be given
as user defined potential by using tables. If i want to give dihedral term as
user defined potential keeping rest of the bonded parameters in their usual
Hello,
I am using Gromacs 4.5 to perform umbrella sampling on CPU. I know that
right now the GPU implementation does not support any pull code. Is it
going to be available soon? Are angular restraints going to be supported
as well?
Thank you
--
Diana Fusco
Graduate Student
Computational
On 5/16/12 11:16 AM, Steven Neumann wrote:
On Wed, May 16, 2012 at 3:38 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
On 5/16/12 10:25 AM, Steven Neumann wrote:
Dear Justin,
I pulled my ligad away of 6nm from the protein and obtained beautiful
On Wed, May 16, 2012 at 3:38 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 5/16/12 10:25 AM, Steven Neumann wrote:
Dear Justin,
I pulled my ligad away of 6nm from the protein and obtained beautiful and
smooth
curve of PMF using 28 windows. Starting from zero kcal/mol corresponding
to
On Wed, May 16, 2012 at 4:20 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 5/16/12 11:16 AM, Steven Neumann wrote:
On Wed, May 16, 2012 at 3:38 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
On 5/16/12 10:25 AM, Steven Neumann wrote:
Dear Justin,
Hi,
I am using the utility g_potential. It takes (among other files) an index
file. At the beginning of the run, it prompts me for a selection from the
index file. Is it possible to make more than one selection, such that the
potential is calculated for each selection, _separately_? If I
On 5/16/12 11:30 AM, Andrew DeYoung wrote:
Hi,
I am using the utility g_potential. It takes (among other files) an index
file. At the beginning of the run, it prompts me for a selection from the
index file. Is it possible to make more than one selection, such that the
potential is
Hi Guys
You know any porgram that can be used to derrive CM3 point charges
thanks
Milinda Samaraweera
University of Connecticut
Department of Chemistry
55 N Eagleville road
unit 3060
Storrs CT
USA--
gmx-users mailing listgmx-users@gromacs.org
Dear Gromacs users,
I am using tabulated potentials
for dihedrals of my system which is of form dih = (1/2)*K[COS
n(phi-phi0)], Here n=3.
I have generated table_d0.xvg by uniformly varying phi as 0.1 from -180
to 180 and calculated the numerical
Hi,
For the simulation of a Protein ligand complex, i obtained the itp topology
of the ligand from PRODRG 2 server and i ran the simulation of the complex
a year back using GROMOS united atom force field by -ff gmx option in
GROMACS 3.3 according to the Drg enzyme tutorial
now i am unable to run
Dear users:
Let us say that I used g_analyze -g -fitfn exp and obtained the exponential
autocorrelation time of a dataset. What does the exponential autocorrelation
time represent? I imagine that it might be the time required to, on average,
obtain a statistically independent sample, or
Dear gromacs users,
I am trying to port in gromacs the CHARMM36 all-atom carbohydrate force
field.
I downloaded the charmm files toppar_carb_apr12.tgz from
http://mackerell.umaryland.edu/CHARMM_ff_params.html
and I converted bonded and nonbonded parameters in gromacs format through
the script
Hi all,
I am using a user defined potential to describe non-bonded
interactions, which describes attractive potential for residues separated
by four or more bonds . Now I want to describe a user defined
potential(repulsive) for atoms falling with in three residues and which are
not
On 5/16/12 2:25 PM, Sarath Kumar Baskaran wrote:
Hi,
For the simulation of a Protein ligand complex, i obtained the itp topology of
the ligand from PRODRG 2 server and i ran the simulation of the complex a year
back using GROMOS united atom force field by -ff gmx option in GROMACS 3.3
Hi Chris,
Probably these links give you simple and clear response for your question
http://idlastro.gsfc.nasa.gov/idl_html_help/Time-Series_Analysis.html
and
http://www.statsoft.com/textbook/time-series-analysis/
HTH
Stephane
--
gmx-users mailing listgmx-users@gromacs.org
Hello,
I want to calculate the pKa shift of a buried aspartic acid residue in my
protein using alchemical free energy perturbation. I do not know how to
represent the individual aspartic acid attached to the protein in the
required couple-moltype entry of the *mdp file. Any suggestions would be
Thank you Stephane.
Unfortunately, neither of those links contains the information that I am
seeking. Those links contain some example plots of autocorrelation functions
including a discussion of time-spans over which the example time-series is
autocorrelated and when it is not, but neither
Dear gmxers,
I have prepared the inputs and tried to run constraint distance pulling on
two-molecule pair. However, one error is output which indicates that two atoms
on the molecule including the pull group are beyond the 1-4 table range. I have
chosen one reference group and one pull group.
On 5/16/12 6:50 PM, xiaowu759 wrote:
Dear gmxers,
I have prepared the inputs and tried to run constraint distance pulling on
two-molecule pair. However, one error is output which indicates that two atoms
on the molecule including the pull group are beyond the 1-4 table range. I have
I'm
Thanks. I think I should have a look at some specific documents to understand
the flow of control.
Namely, to understand what is purpose of the subroutines in src/mdlib/. But
I could not find such
information in the Gromacs user manual. Do anyone know such an document?
Thanks.
Hello everyone,
I am trying to estimate the thermodynamic expression, dP/dw at
constant V and T, for my polymer-solvent system. Where P is the
pressure, w is the mass fraction, V volume and T temperature. I guess
this task can not be done by MD, as for constant Volume, pressure is
meaningless.
Dear Tsjerk
Thank you
Sogol
From: Tsjerk Wassenaar tsje...@gmail.com
To: Kowsar Bagherzadeh kw_bagherza...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Sent: Wednesday, May 16, 2012 2:46 PM
Subject: Re: [gmx-users] Spherical shaped
Hi,
if you want to calculate the potential of some groups (0, 3, 11), using
make_ndx to creat a new group consisting of these groups. Then running
g_potential.
Cuong
2012/5/16 Andrew DeYoung adeyo...@andrew.cmu.edu
Hi,
I am using the utility g_potential. It takes (among other files) an
Respected sir,
thanks for your kind reply...
i applied position restrain during nvt step sir..
Thanking you,
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