Hi!
I need an advice concerninng topology building of such substance like
cyclosporine A. I've tried to make it with antechamber tool, cause I wanted
to use amber99sb forcefield. But the program gave me an error in the
begining and no results in the end after 12 hours of calculations ))) Can
you
Justin
Sure, you could do all of it within a shell script that loops the commands
and checks the printed output.
As I understood in that iterations only step with scalling by factor 0.95
and futher energy minimization must be included until desired S per lipid
will be reached. Could you
I am a new gromacs user. I wanted to simulate a membrane protein without the
lipid bilayer using the IMM1 force field of CHARMM27. I really would
appreciate if someone can help me solve this or direct me towards implicit
solvation tutorial in gromacs
Regards,
Soumya
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gmx-users mailing
Check the below link:
http://www.gromacs.org/Documentation/Terminology/Implicit_Solvent
On Mon, Oct 17, 2011 at 13:47, Soumya Lipsa Rath
soumyalips...@gmail.com wrote:
I am a new gromacs user. I wanted to simulate a membrane protein without the
lipid bilayer using the IMM1 force field of
Dear all,
I would like to simulate my protein in a lipid bilayer using gromacs 4.5.4,
and a forcefield of gromos96. However i don't have the topologies files for
lipid bilayer for POPE and DMPE. Anybody knows where can i get the
topologies file for POPE and DMPE ? Before that, i had actually
There is already tutorial for creating lipid bilayer and insertion of
protein into that for GROMACS
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
Why you have used Charmmgui I am not able to understand.
You can get some useful topologies from
Dear users,
For simulating a protein at high temperature (more than 300K,
less than 400K) using OPLSAA forcefield, what are the parameters
other than Temperature that need to be taken care of?
Does the energy minimization step also needs to be done at high
temperature? (here my aim is not to
As far as I know we do energy minimization at room temperature only.
Only during equilibration
(NVT and NPT) we use high temperature for maintaining proper density
before starting the final production run.
On Mon, Oct 17, 2011 at 15:15, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
For
Hi Roy,
PE lipids are less frequently used than PC ones and there are fewer
topologies available. Also it has been shown that using the Berger PC
lipid topologies (the most frequently used united-atom PC lipids) and
simply changing the CH3 atoms in the head group to H is not a good
approach
Thank you,
What about the pressure that need to be used at that temperature
(for a system of a protein in tip4p water)
Thank you
With Regards
Kavya
On Mon, Oct 17, 2011 at 3:29 PM, bipin singh bipinel...@gmail.com wrote:
As far as I know we do energy minimization at room temperature only.
Nilesh Dhumal wrote:
Hello,
I have system with solute is surrounded by 256 solvent molecules. I run
the simulation for 20 ns. I save the snap shot at 500 ps using following
command.
trjconv -f 3.trr -s 3.tpr -n 500-1.ndx -b 500.0 -e 501.0 -dt 1.0 -pbc
nojump -center -o 500-11.pdb
I tried
James Starlight wrote:
Justin
Sure, you could do all of it within a shell script that loops the
commands and checks the printed output.
As I understood in that iterations only step with scalling by factor
0.95 and futher energy minimization must be included until desired S per
bipin singh wrote:
As far as I know we do energy minimization at room temperature only.
Energy minimization is (theoretically) at 0 K, as there are no velocities and it
is not a true dynamical process.
Only during equilibration
(NVT and NPT) we use high temperature for maintaining proper
Kavyashree M wrote:
Thank you,
What about the pressure that need to be used at that temperature
(for a system of a protein in tip4p water)
The set pressure should reflect whatever system you are trying to model.
-Justin
Thank you
With Regards
Kavya
On Mon, Oct 17, 2011 at 3:29 PM,
Well,as I found in literatures people have used same( 1 atm) pressure
at high temperature simulations(NPT simulations).
with different water models.As most of the force field parameters are
determined generally at 300K and 1 atm.
What would be the the possible drawbacks of using the same
James,
As the consequence the correct orientation of the peptide in the membrane as
well as futher solvation are caused many questions :)
Firsly, following by tutorial guide I've done orientation of KALP peptide in
the membrane by
1- perl inflategro.pl confout.gro 0.95 DPPC 0
I have not understood what you mean by
Energy minimization is (theoretically) at 0 K, as there are no velocities
and it is not a true dynamical process.
It is clear to me that at 0K there would be no velocities but then why
during minimization we expect
some conformational rearrangement of side
James Starlight wrote:
James,
As the consequence the correct orientation of the peptide in the
membrane as well as futher solvation are caused many questions :)
Firsly, following by tutorial guide I've done orientation of KALP
peptide in the membrane by
1- perl inflategro.pl
In the energy minimisation step, any conformational rearrangement taking
place is not a function of time, it is just an algorithm for reaching a
basin of minimum energy:
(http://www.gromacs.org/Documentation/Terminology/Energy_Minimisation),
hence there are not velocities in the atoms of the
On 17/10/2011 10:58 PM, bipin singh wrote:
I have not understood what you mean by
Energy minimization is (theoretically) at 0 K, as there are no velocities
and it is not a true dynamical process.
It is clear to me that at 0K there would be no velocities but then why
during minimization we expect
On 17/10/2011 5:01 PM, Алексей Раевский wrote:
Hi!
I need an advice concerninng topology building of such substance like
cyclosporine A. I've tried to make it with antechamber tool, cause I
wanted to use amber99sb forcefield. But the program gave me an error
in the begining and no results in
Dear All,
I tried to post this once before. In any case;
Basically I am doing free energies quickly, and then plan on doing pull runs.
This former is simply EQ all the way to NPT (700-1000 PS +), then a 5 PS run
for the bound, then unbound system. Energy differences are taken as the
--- [CMakeCache.txt] -
...
//Flags used by the compiler during all build types
CMAKE_CXX_FLAGS:STRING=' -msse2 -ip -funroll-all-loops -std=gnu99 '
//Flags used by the compiler during release builds.
Dear gmx-user,
I would like to simulate an isolated drop of water (without PBC). To prevent
water molecules form evaporation I would like to create a spherical constraint
around the system. In recent article in PNAS (Caleman, Hub, van Maaren, van der
Spoel, v. 108, 6838 (2011)) where the
Ok, James thank you
It seems that I should to wite some script for too many iterations e.g
perl inflategro.pl minimized1.gro 0.95 DPPC 0 shrinked1.gro 5 area_shrink1.dat
grompp -f minim.mdp -c shrinked1.gro -p topol.top -o minimized2.tpr
mdrun -v -deffnm minimized2
perl inflategro.pl
On 17/10/2011 11:41 PM, Mikhail Stukan wrote:
Dear gmx-user,
I would like to simulate an isolated drop of water (without PBC). To
prevent water molecules form evaporation I would like to create a
spherical constraint around the system. In recent article in PNAS
(Caleman, Hub, van Maaren,
James Starlight wrote:
Ok, James thank you
It seems that I should to wite some script for too many iterations e.g
perl inflategro.pl http://inflategro.pl minimized1.gro 0.95 DPPC 0
shrinked1.gro 5 area_shrink1.dat
grompp -f minim.mdp -c shrinked1.gro -p topol.top -o minimized2.tpr
mdrun
Hi Mikhail,
we hard-coded the flat-bottom potential into bondfree.c which is in
src/gmxlib. I send you the source file in a separate e-mail.
The patch will replace all position restraints by a flatt-bottom
spherical potential with a flat radius of 1.4nm. If you want a different
radius
Hello,
The set pressure should reflect whatever system you are trying to model.
This statement is not very clear to me.. But when the mdout.mdp file after
grompp
during energy minimization is examined it says -
gen-vel = no
gen-temp = 300
gen-seed
Justin,
I have 26 solute atoms and 3302 solvent atoms in my sytems (total 3328
atoms).
1. trjconv -f 3.trr -s 3.tpr -pbc mol -b 400 -e 600 -dt 1 -n 500-1.ndx -o
4-600.xtc
here I choose group 0:system (3328 atoms)
2. trjconv -f 4-600.xtc -s 3.tpr -n 500-1.ndx -center -o 4-600-1.xtc
For
Kavyashree M wrote:
Hello,
The set pressure should reflect whatever system you are trying to model.
This statement is not very clear to me.. But when the mdout.mdp file
after grompp
during energy minimization is examined it says -
gen-vel = no
gen-temp
Nilesh Dhumal wrote:
Justin,
I have 26 solute atoms and 3302 solvent atoms in my sytems (total 3328
atoms).
1. trjconv -f 3.trr -s 3.tpr -pbc mol -b 400 -e 600 -dt 1 -n 500-1.ndx -o
4-600.xtc
here I choose group 0:system (3328 atoms)
2. trjconv -f 4-600.xtc -s 3.tpr -n 500-1.ndx -center
Hello,
Yes, I have come across that but If the temperature is below
the boiling point its fine. But if it crosses the boiling temperature
in order keep the water as liquid isnt it necessary to increase the
pressure. I understand that the water models do not exactly predict
the transition
Hello,
I am sorry those were two different questions.. I wanted to know what
this statement actually mean?
The set pressure should reflect whatever system you are trying to model.
Thank you
With Regards
Kavya
I don't see the connection to my comment about pressure, but I'll address
this
Kavyashree M wrote:
Hello,
I am sorry those were two different questions.. I wanted to know what
this statement actually mean?
The set pressure should reflect whatever system you are trying to model.
You haven't fully explained what exactly you're trying to do yet, so I'm taking
a stab
In 2nd step I choose system instaed of solvent.
I could not make the solute at the center.
Thanks
NIlesh
On Mon, October 17, 2011 11:05 am, Justin A. Lemkul wrote:
Nilesh Dhumal wrote:
Justin,
I have 26 solute atoms and 3302 solvent atoms in my sytems (total 3328
atoms).
1.
Ok, The protein I am going to simulate is from a hyperthermophilic organism
which lives in deep oceanic thermal vents. so in the deep vents the pressure
will be enormous. even though I do not have much information about the
magnitude of pressure in that site and inside the cell of that organism..
Nilesh Dhumal wrote:
In 2nd step I choose system instaed of solvent.
I could not make the solute at the center.
Don't use -b and -e when running trjconv. I have found that PBC routines are
not always correctly applied when parsing out sections of the trajectory. This
can affect your
Kavyashree M wrote:
Ok, The protein I am going to simulate is from a hyperthermophilic organism
which lives in deep oceanic thermal vents. so in the deep vents the pressure
will be enormous. even though I do not have much information about the
magnitude of pressure in that site and inside the
Dear Gmx Users,
I would like to calculate the interaction energy (LJ and
electrostatic) between each residue and my ligands (10 ligands in the
system). I would like to see what is the contribution of electrostatic and
vdW interactions between ligand and each of my residue. I thought to use
Thanks Justin,
Still solute is not at center.
Nilesh
On Mon, October 17, 2011 11:27 am, Justin A. Lemkul wrote:
Nilesh Dhumal wrote:
In 2nd step I choose system instaed of solvent.
I could not make the solute at the center.
Don't use -b and -e when running trjconv. I have found
No I need your help in any way, antechamber is not only the way I could do
it, I think...I just showed you that I tried something before I wrote you a
letter. It is not necessary to use amber forcefield, but I don't think that
prodrg is a good choice for this task, though the only modification of
Dear Justin,
After 20 iterations I've obtained structure like this
http://www.sendspace.com/file/gyyj38
I suppose that this variat is more closely to correct form :)
But during solvation via GenBox I've obtained that error
One of the box vectors has become shorter than twice the cut-off
Hi Pramod,
Please keep all general queries and questions on the GROMACS mailing list.
For CHARMM27, POPC can be found as an rtp entry. This means a topology
can be generated using pdb2gmx. It is easiest if you do this using one
POPC lipid and then make an itp from the top. A CHARMM POPC
Steven Neumann wrote:
Dear Gmx Users,
I would like to calculate the interaction energy (LJ and
electrostatic) between each residue and my ligands (10 ligands in the
system). I would like to see what is the contribution of electrostatic
and vdW interactions between ligand and each of my
James Starlight wrote:
Dear Justin,
After 20 iterations I've obtained structure like this
http://www.sendspace.com/file/gyyj38
I suppose that this variat is more closely to correct form :)
I can't access the file, so I don't know. 20 iterations still doesn't sound
like enough for the
Nilesh Dhumal wrote:
Thanks Justin,
Still solute is not at center.
Is your reference frame (i.e. the .tpr file) centered? If not, centering likely
won't work as desired. I assumed that it was centered, per normal system
building procedures.
-Justin
Nilesh
On Mon, October 17, 2011
Hey :)
The reference plays no role in centering. But I guess that Nilesh expects
centering of the solute w.r.t. to the solvent, or is looking at the wrong
center (tric/rect).
Cheers,
Tsjerk
On Oct 17, 2011 7:06 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Nilesh Dhumal wrote: Thanks Justin,
On Fri, Oct 14, 2011 at 9:11 AM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 14/10/2011 10:12 AM, Ben Reynwar wrote:
Hi gromacs list,
I'm about to start some REMD simulations using generalized Born
solvent on a protein of about 5000 atoms. I have two questions, the
first of which is
Hi Justin,
Using make_ndx on the trajectory file (output from trjorder), and listing out
different lipids i did see the lipids arranged based on the distance from
protein.
Now i want to choose lipids within 0.5nm from protein for my analysis. As in
the index file the lipids are listed based
Poojari, Chetan wrote:
Hi Justin,
Using make_ndx on the trajectory file (output from trjorder), and listing out
different lipids i did see the lipids arranged based on the distance from
protein.
Now i want to choose lipids within 0.5nm from protein for my analysis. As in
the index file
Hello fellow GMX users,
I've been digging in the archives and haven't yet found a good response to
this question, so I thought I'd ask again, since I see from a post just last
month others are still interested in this subject as well. Is it possible in
Gromacs to periodically update/change the
Ya, I want to center solute w.r.t to the solvent.
I have more question, if I want to save the coordinates of a snapshot with
no pbc effect, can I use -pbc nojump in trjconv.
nilesh
On Mon, October 17, 2011 1:34 pm, Tsjerk Wassenaar wrote:
Hey :)
The reference plays no role in centering. But
Justin
I can't access the file, so I don't know. 20 iterations still doesn't
sound like enough for the tutorial system, unless you shrunk faster than
what was recommended.
20 iteration was a simple example. It means that many iterations produced
more accuracy results in comparison to
Hello,
I have saved the coordinates of snapshot from trajectory in pdb file.
The dimesnion of box in pdb file are
32.805 32.805 32.805 90.00 90.00 90.00 P 1
I am trying to find atoms close to center of box.
there are atoms whose distance from center is more that ~17 A. My center
James Starlight wrote:
Justin
I can't access the file, so I don't know. 20 iterations still
doesn't sound like enough for the tutorial system, unless you shrunk
faster than what was recommended.
20 iteration was a simple example. It means that many iterations
produced more
Hi Nilesh,
To center the solute with respect to the solvent, first center the
solute in the box, and then put the solvent in the box. Mind that that
involves two passes of trjconv.
If 'no pbc effect' means no wrapping over the boundaries, yes you can
use -dump with -pbc nojump to save a
Hi Gmxers,
Is there a way I can check all the kinds of solvents in gromacs? Apart from
water, ethanol, ...,
are there any Glycerol, Treholose,
Thanks,
Yao
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Yao Yao wrote:
Hi Gmxers,
Is there a way I can check all the kinds of solvents in gromacs? Apart
from water, ethanol, ...,
are there any Glycerol, Treholose,
There likely aren't many. Anything available would be in the force field
subdirectory for whatever force field you want.
On 18/10/2011 4:58 AM, Ben Reynwar wrote:
On Fri, Oct 14, 2011 at 9:11 AM, Mark Abrahammark.abra...@anu.edu.au wrote:
On 14/10/2011 10:12 AM, Ben Reynwar wrote:
Hi gromacs list,
I'm about to start some REMD simulations using generalized Born
solvent on a protein of about 5000 atoms. I have
On 18/10/2011 7:05 AM, Nilesh Dhumal wrote:
Hello,
I have saved the coordinates of snapshot from trajectory in pdb file.
The dimesnion of box in pdb file are
32.805 32.805 32.805 90.00 90.00 90.00 P 1
I am trying to find atoms close to center of box.
there are atoms whose distance
On 18/10/2011 5:40 AM, J. Nathan Scott wrote:
Hello fellow GMX users,
I've been digging in the archives and haven't yet found a good
response to this question, so I thought I'd ask again, since I see
from a post just last month others are still interested in this
subject as well. Is it
On 18/10/2011 2:57 AM, ??? wrote:
No I need your help in any way, antechamber is not only the way I
could do it, I think...I just showed you that I tried something before
I wrote you a letter. It is not necessary to use amber forcefield,
but I don't think that prodrg is a good
I used -pbc nojump to remove pbc effect.
trjconv 3.trr -s 3.tpr -pbc nojump -o 500-11.pdb
Basically I want to find the conformer close to center of box.
Nilesh
On Mon, October 17, 2011 6:36 pm, Mark Abraham wrote:
On 18/10/2011 7:05 AM, Nilesh Dhumal wrote:
Hello,
I have saved the
On 18/10/2011 11:48 AM, Nilesh Dhumal wrote:
I used -pbc nojump to remove pbc effect.
Please read trjconv -h about -pbc nojump. If molecules can't jump, then
they must diffuse. You can't have both.
Mark
trjconv 3.trr -s 3.tpr -pbc nojump -o 500-11.pdb
Basically I want to find the
Dear All:
I am using g_membed command to insert a protein into a membrane
bilayer, however, when I run the following command:
g_membed -f input.tpr -p topology.top -xyinit 0.1 -xyend 1.0 -nxy 1000
I encountered the following errors:
Program g_membed, VERSION 4.5.4
Source code file:
how can i do if i want to do Shell Molecular Dynamics(Drude ) with
GROMACS VERSION 4.0.7?
I only find you should set emtol: (1.0) niter: (20) fcstep: (0)
[ps2] in *.mdp file .(GROMACS_4.0 manual)
But how i can write the *.gro and *.top ? Are they smae with the
traditional MD?
And i can not
On 18/10/2011 2:08 PM, mirc...@sjtu.edu.cn wrote:
Dear All:
I am using g_membed command to insert a protein into a membrane
bilayer, however, when I run the following command:
g_membed -f input.tpr -p topology.top -xyinit 0.1 -xyend 1.0 -nxy 1000
I encountered the following errors:
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