Hello, everyone,
I am reviving a discussion I started about a month back.
http://gromacs.5086.n6.nabble.com/Water-molecules-cannot-be-settled-why-tt4998059.html
I thought that I would try to work around the problem by only proceeding
with those simulations that didn't crash, but I've reached
Hello all,
I m performing a pulling simulation on my Protein-Mg-GTP complex. I
have considered pulling between the GTP and a residue of protein.
The pull code in the .mdp file im using is as follows:
; Pull code
pull= umbrella
pull_geometry = distance ; simple distance increase
pu
Hi,
You didn't write what your coupling groups are.
But using tau_t=0 would scale velocity to 0 in a single step and they would
stay close to 0.
Cheers,
Berk
> Date: Tue, 10 Jul 2012 21:04:08 -0700
> From: inons...@tau.ac.il
> To: gmx-users@gromacs.org
> Subject: [gmx-users] נושא: RE: Disco
Hi John,
Check where the unsettling water molecule is placed. If it's in the
protein. that may be the cause of the problem. Otherwise, it's some of
the other stuff you're doing, but rule out the simple things first.
Cheers,
Tsjerk
On Wed, Jul 11, 2012 at 10:12 AM, John Ladasky
wrote:
> Hello,
Dear Gromacs Users,
I have a system consists of cyclohexan, pentanol, surfactant and water
in MARTINI coarse-grained ff, when I do pr.mdp for this system
(posre.itp file is only for surfactant), water molecules are not
distributed and are aggregated in one place in the box.
I don't know what shoul
Dear Gromacs Users,
I have a system consists of cyclohexan, pentanol, surfactant and water
in MARTINI coarse-grained ff, when I do pr.mdp for this system
(posre.itp file is only for surfactant), water molecules are not
distributed and are aggregated in one place in the box.
I don't know what shoul
Hi all,
I'm going to do the step 3 in Justin's tutorial (Lysozyme in water) . In this
step, the solvation is accomplished through this command:
genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
in which that spc216.gro is used. In first step I had used the TIP3P water
mode
Hi,
I had this problem too.
unfortunately gmx not included tip3p model of water anymore.
You have two ways.
1.using spc216 that gmx offers or
2.Buil your system in Ambertools (leap) and convert your .prmtop and
.inpcrd files to .top and .gro
if you persist on using tip3p water model i suggest you t
Hi All!
I want to use Implicit solvent to simulate a nucleic acid sequence.
How can I do it?
I use this command:
genion -s ions.tpr -o nucleic_ions.gro -p nucleic.top -pname K+ -nname
CL -neutral -conc 0.1
ions.tpr file is same as umbrella sampling tutorial.
I got this error message:
Fatal error:
Hi everybody,
I did a minimization of my structure. But the output seems a bit strange
for me, since my input was the protein with its membrane in a box like
this:
# = box P = Protein M=Membrane
#
# #
# MM#
# #
# #
# #
#
B
On 7/11/12 5:36 AM, Shima Arasteh wrote:
Hi all,
I'm going to do the step 3 in Justin's tutorial (Lysozyme in water) . In this
step, the solvation is accomplished through this command:
genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
in which that spc216.gro is used. I
On 7/11/12 6:00 AM, amir abbasi wrote:
Hi All!
I want to use Implicit solvent to simulate a nucleic acid sequence.
How can I do it?
I use this command:
genion -s ions.tpr -o nucleic_ions.gro -p nucleic.top -pname K+ -nname
CL -neutral -conc 0.1
ions.tpr file is same as umbrella sampling tutori
On 7/11/12 6:13 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I did a minimization of my structure. But the output seems a bit strange
for me, since my input was the protein with its membrane in a box like
this:
# = box P = Protein M=Membrane
#
# PPP
Thanks Justin,
But I want to neutralize my system in implicit solvent.
In Amber I had use Debye screening but in gromacs I don't know what should I do.
On Wed, Jul 11, 2012 at 2:45 PM, Justin A. Lemkul wrote:
>
>
> On 7/11/12 6:00 AM, amir abbasi wrote:
>>
>> Hi All!
>> I want to use Implicit so
On 7/11/12 6:19 AM, amir abbasi wrote:
Thanks Justin,
But I want to neutralize my system in implicit solvent.
In Amber I had use Debye screening but in gromacs I don't know what should I do.
From my understanding, this remains an unresolved issue.
-Justin
On Wed, Jul 11, 2012 at 2:45 PM,
Hi Justin,
ah okey. Thank you.
And I have another question. Why is the protein in the corner of the box
and not in the middle?
I thought I centered it with the command:
editconf -f wholeProtein.gro -o 3m71_box.gro -center 4.59340 4.59470
5.17330 -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut
O
On 7/11/12 7:12 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
ah okey. Thank you.
And I have another question. Why is the protein in the corner of the box
and not in the middle?
I thought I centered it with the command:
editconf -f wholeProtein.gro -o 3m71_box.gro -center
Yes I tried the command you wrote but it is still in the corner of the box.
Is there anything else I can do?
The coordinates I used to center the protein are the ones which are in the
last line of the .gro file.
Thank you
>
>
> On 7/11/12 7:12 AM, reising...@rostlab.informatik.tu-muenchen.de wrot
On 7/11/12 7:34 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Yes I tried the command you wrote but it is still in the corner of the box.
Is there anything else I can do?
The coordinates I used to center the protein are the ones which are in the
last line of the .gro file.
The last
Dear All,
Could anyone please suggest me some article or information that contains
force field parameters (gromacs53A6) for acetyl Coenzyme A
Thanks in advance.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are a
On 7/11/12 8:18 AM, Padmanabhan Anbazhagan wrote:
Dear All,
Could anyone please suggest me some article or information that contains
force field parameters (gromacs53A6) for acetyl Coenzyme A
Google turned up:
http://compbio.biosci.uq.edu.au/atb/download.py?molid=5470
-Justin
--
=
Hi everybody,
I wanted to ask if there is a possibility to tell pdb2gmx which residues I
want to be protonated or not.
So that I can for example say HIS at position 29 shell be protonated twice.
I need this for further electrostatic analysis.
Thank you,
Eva
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gmx-users mailing listgmx-use
On 7/11/12 10:24 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I wanted to ask if there is a possibility to tell pdb2gmx which residues I
want to be protonated or not.
So that I can for example say HIS at position 29 shell be protonated twice.
I need this for further e
Please keep the discussion on the gmx-users mailing list.
On 7/11/12 10:43 AM, panbazha wrote:
Dear Justin,
That file was generated by me in ATB, The issue is when i looked into
the united atom itp file, I found many bonds and angles has not determined. So,
just wondering if there are any publi
This is not really true. It is perfectly appropriate to use spc216.gro with
the tip3p water model since any spacing differences will settle out during
npt equilibration anyway.
On 2012-07-11 02:28:52PM +0430, amir abbasi wrote:
> Hi,
> I had this problem too.
> unfortunately gmx not included tip3
Dear gmx friends,How much time should have been spent in NPT equilibrium for a
system composed of protein and water? In Justin's tutorial, I saw it is 100 ps
for a system composed of Lysozym and water.
Thanks in advance.
Sincerely,
Shima
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gmx-users mailing listgmx-users@gromacs.org
htt
On 7/11/12 2:08 PM, Shima Arasteh wrote:
Dear gmx friends,How much time should have been spent in NPT equilibrium for
a system composed of protein and water? In Justin's tutorial, I saw it is
100 ps for a system composed of Lysozym and water.
Long enough for the observables of interest to c
Dear Gromacs,
I'm trying to build a QM/MM with gromacs as MM.
The thing would be run by ASE-simulation environment
(https://wiki.fysik.dtu.dk/ase/).
Question: I'm trying to get the potential energy of a single atomic
configutation.
Is it possible to get the potential energy of a given configurati
On 7/11/12 3:14 PM, Markus Kaukonen wrote:
Dear Gromacs,
I'm trying to build a QM/MM with gromacs as MM.
The thing would be run by ASE-simulation environment
(https://wiki.fysik.dtu.dk/ase/).
Question: I'm trying to get the potential energy of a single atomic
configutation.
Is it possible to
Dear Gromacs Users!
I want to perform my simulation under conditions with collisional
thermostat (where each atom is bombarded by virtual particles with
Maxwell speed distribution) instead of thermostat with alternate
friction ( like Nose Hoover which I'm using after my system have been
equilibra
Hi,
I am trying to perform a NVE simulation of water at 300K using the TIP4P
potential, with 309 molecules.
I do 50ps of equilibration with a Nose-Hoover thermostat with tau_t = 1
first to get the water at 300K.
However, when I then do my main run, the temperature suddenly jumps up at
the beg
Dear All,
I am simulating a protein in gromacs with amber force field. The
protein shows maximum biological activity at pH 5.0 and at pH 7.4 it
shows no activity. So whichever biological process I am going to model
should be at the biologically active pH . So can anyone suggest me
1) how to get
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