> Date: Wed, 11 Apr 2012 08:38:05 -0400
> From: "Justin A. Lemkul"
> Subject: Re: [gmx-users] g_wham problem with negative COM differences
> To: Discussion list for GROMACS users
> Message-ID: <4f857b2d.3050...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Anni Kau
Hi all: I'm trying to run a coarse grained system with 3 different
kind of particles, lets call them "A", "B" and "C", and the
interactions between them are set by means of 3 tabulated potentials
(not LJ, totally customized ones). I want to introduce 1-4
interactions with the -tablep optional argum
Thanks Mark. I have several polymer chains (single polymer type) each
having 362 atoms. So in order to exclude all nonbonded interactions of
a chain with itself I need to add about 362 lines in the top file.
[exclusions]
1 2 3 362
2 3 4 362
3 4 5 ...362
.
358 .. 362
.
.
360 361 362 (this i
On 13/04/2012 3:08 AM, Qinghua Liao wrote:
Dear gmx users,
I tried to apply distance restraints to my system, but I found that it
failed because the distance between the restraints atoms in the last
frame is bigger than what we want.
Distance restraints aren't magic. There has to be an acces
On 13/04/2012 2:48 AM, Laura Leay wrote:
All,
I'm trying to run a tabulated soft core potential with the form V = A
+ Br^2 + Cr^3 up to about r=0.1 A and the normal LJ 6-12 potential
after this.
I've chosen the parameters of this equation to be the same for all
atoms in my system (a polymer
On 13/04/2012 10:44 AM, Juliette N. wrote:
Hello all,
I am trying to exclude a nonbonded interactions on the polymer chains using
grompp -f old.mdp -c old_em.gro -p nrexcl_new.top -o new.tpr
and mdrun -rerun command. but when I issue the command above grompp
takes many hours to finish and at t
On 13/04/2012 2:36 AM, J. Nathan Scott wrote:
Hi all,
I had a very quick question I couldn't find an exact answer for that
I'm sure someone here can answer very easily. The Gromacs website says
(http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File):
"A .cpt file is produced by mdru
Hello all,
I am trying to exclude a nonbonded interactions on the polymer chains using
grompp -f old.mdp -c old_em.gro -p nrexcl_new.top -o new.tpr
and mdrun -rerun command. but when I issue the command above grompp
takes many hours to finish and at the end grompp crashes (Killed).
This even lea
Hello. You have to check whether the formyl residue is defined with
other name in the force field files. If not, you have to get the
parameters for it.
Best regards
Lucio Montero
El jue, 12-04-2012 a las 00:40 -0700, Shima Arasteh escribió:
> Dear Gromacs friends,
>
>
> I attached my .pdb file in
Acoot Brett wrote:
Dear All,
For the on-line tutorial of *Justin Lemkul on *NPT equilibriation
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/07_equil2.html),
if we extend the npt simulation time from 100 ps to 200 ps, is any
possibility that the black pre
Hi Sai,
you have to concider the protein and ligand strucure togather (Docked
structure ),
After these follow the link
(
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
)
With Best Wishes,
Rama
On Thu, Apr 12, 2012 at 5:13 PM, sai nitin wrote:
> hi ra
Dear All,
For the on-line tutorial of Justin Lemkul on NPT equilibriation
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/07_equil2.html),
if we extend the npt simulation time from 100 ps to 200 ps, is any possibility
that the black pressure curve would be smoo
Hi priya
http://www.gromacs.org/Documentation/Gromacs_Utilities/make_ndx these
link may be help to you
i like to know how to calculate index groups for my micelles..
since i am having two micelles , one having 8molecules and another having
2molecules.. residue number for that 2molecule micelle i
Shima Arasteh wrote:
Dear Justin,
ok. But I have to regenerate a job done sometime ago, that's why I have
to use this ff. Am I supposed to use the seventeenth option?
Yes, option 17 is the Gromos87-derived united atom force field that was once
called "ffgmx."
-Justin
Cheers,
Shima
Dear Justin,
ok. But I have to regenerate a job done sometime ago, that's why I have to use
this ff. Am I supposed to use the seventeenth option?
Cheers,
Shima
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Thursday, April 12, 2012 9:
Qinghua Liao wrote:
Dear gmx users,
I tried to do simulations of a small peptide in vacuum, I found that it
failed to be run in parallel, even when I use only 8 cores.
My system only have hundreds of atoms. the problem may be resulted from
domain decomposition. When I choose particle
decompo
Dear gmx users,
I tried to do simulations of a small peptide in vacuum, I found that it
failed to be run in parallel, even when I use only 8 cores.
My system only have hundreds of atoms. the problem may be resulted from
domain decomposition. When I choose particle
decomposition method, for small s
Dear gmx users,
I tried to apply distance restraints to my system, but I found that it
failed because the distance between the restraints atoms in the last frame
is bigger than what we want. Here are the parameters for distance
restraints in the topology file:
[ distance_restraints ]
; ai aj ty
All,
I'm trying to run a tabulated soft core potential with the form V = A + Br^2 +
Cr^3 up to about r=0.1 A and the normal LJ 6-12 potential after this.
I've chosen the parameters of this equation to be the same for all atoms in my
system (a polymer containing carbon, nitrogen and hydrogen). I
Marzinek, Jan wrote:
*From:* Shima Arasteh [shima_arasteh2...@yahoo.com]
*Sent:* Thursday, April 12, 2012 4:53 PM
*To:* Marzinek, Jan
*Subject:* Re: [gmx-users] Gromos87
Dear Jan,
I downloaded the file and put it
Hi all,
I had a very quick question I couldn't find an exact answer for that
I'm sure someone here can answer very easily. The Gromacs website says
(http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File):
"A .cpt file is produced by mdrun at specified intervals (mdrun -cpt),
and conta
From: Shima Arasteh [shima_arasteh2...@yahoo.com]
Sent: Thursday, April 12, 2012 4:53 PM
To: Marzinek, Jan
Subject: Re: [gmx-users] Gromos87
Dear Jan,
I downloaded the file and put it in my working space but does not appear in my
force filed selections? How c
Hi Shima,
It would be number 17, but as you can see on the prefix, its deprecated (in
other words outdated) and should not be used anymore (unless you really have to
for some reason). Why not try a more modern force field?
Cheers,
Felix
Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Shima Arasteh [shima_arasteh2...@yahoo.com]
Sent: Thursday, April 12, 2012 4:05 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] Gromos87
Dear friends,
I'd like to use g
Dear friends,
I'd like to use gormos87 force field in my simulation. Which force field am I
supposed to select?
1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24,
1999-2012, 2003)
2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
3: AMBER96 protein, nucleic
priya thiyagarajan wrote:
hello sir,
thanks for your kind reply..
in another folder i resubmitted my mdrun from starting time..
i reduced my time step..
i kept my time step = 0.001
this is my md.mdp file
title= Gromacs43a1 lipopeptide MD
; Run parameters
integrator= md
hi rama david,
Thank you for suggestion i looked up how to convert docked structure into
PDB file it is described here
http://autodock.scripps.edu/faqs-help/faq/is-there-a-way-to-save-a-protein-ligand-complex-as-a-pdb-file-in-autodock
But i have one doudt about which structure to take should i c
Hi Catherine,
I did explain this already:
>> > 1 0.602921
Cosine content for first pc
>> > 2 0.011185
Cosine content for second pc
>> > 3 0.0659901
Cosine content for third pc
>> > 4 0.425943
...
>> > 5 0.204306
...
>> > 6 0.439315
...
>> > 7 0.0288551
...
>> > 8 0.0830944
leila karami wrote:
Dear Justin
I'm using your script for obtaining %exist of hydrogen bonds.
When I use ./hb.pl structure.pdb -map hbmap.xpm -index hbond.ndx, I
encountered with
No -map specified!
I noted to points being at the begining of script:
# 1. coordinate file (for atom naming
Dear Justin
I'm using your script for obtaining %exist of hydrogen bonds.
When I use ./hb.pl structure.pdb -map hbmap.xpm -index hbond.ndx, I
encountered with
No -map specified!
I noted to points being at the begining of script:
# 1. coordinate file (for atom naming) - MUST be a .pdb file
Thank you very much Tsjerk,
I under cosine content much better now.
When you means "that only makes sense for one Pc, the analysis is thus
performed per component", could you mind to explain more?
I did the cosine content analysis with the following command "
/usr/local/gromacs/bin/g_analyze_d
Hi Catherine,
> When we use cosine content to determine if our simulation are converged or
> not, should I
You can't use the cosine content to determine if a simulation is
converged. You can only use it to determine whether the simulation is
not converged, which is quite a different thing.
> (1)
Hi Catherine,
> Am I correct to say the cosine content of the first three principal
> components are as follows:
Yes.
Cheers,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike
Dear experts in the field,
When we use cosine content to determine if our simulation are converged or not,
should I
(1) sum all the first three principal components together or examine
individually?
(2) If I expect the first 10 ns is the equilbrium period, while the other 20 ns
as the producti
Dear Tsjerk,
Am I correct to say the cosine content of the first three principal components
are as follows:
PC1 : 0.602921
PC2: 0.011185
PC3:
0.0659901
As my coscont.xvg file is as follows:
> > @title "Cosine content"
> > @xaxis label "set / half periods"
> > @yaxis label "cosine
hello sir,
thanks for your kind reply..
i like to know how to calculate index groups for my micelles..
since i am having two micelles , one having 8molecules and another having
2molecules.. residue number for that 2molecule micelle is 2 and 7..
can you help me how to form index group for this t
According to this
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html)
tutorial, you have to combine your target protein and your ligand.
First of all, use pdb2gmx to generate gromacs topologies and coordinates.
After that merge protein.gro with ligand.gro. Do
Hi sai,
you have to used docked structure to simulation .
1st convert the dock structure ,that you concider imptortant for
your further study to pdb file (As you used autodock for docking ).
Then perform MD on that structure.
Have a nice day...
On Thu, Apr 12, 2012 at 2:14 PM, sai nitin wrote:
Hi gontchar,
I have done docking analysis using autodock using that ligand and binding
site but i want to do molecular dynamics (MD) using gromacs of same ligand
and binding site of my protein. Thats why i want to know how to place
ligand in specific binding site and run MD using gromacs.
Thanks,
I think you have to use some special programm for this purpose.
AutoDock, for example, will be the right choice.
2012/4/12 sai nitin :
> Hi all,
>
> I am working on protein - ligand molecular dynamics simulation using
> gromacs. I have a protein in which i know binding site which is composed of
>
Hi all,
I am working on protein - ligand molecular dynamics simulation using
gromacs. I have a protein in which i know binding site which is composed of
5 residues and i have one ligand i have to place this in binding site.
Can any body tell me how to do place this ligand to binding site
Thanks
Hi Shima,
It seems like this residue is not parameterized for the force field you want to
use. Maybe check
http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks if
you can find it under a different name. If not, have a look at
http://www.gromacs.org/Documentation/How-tos/Ad
Dear Gromacs friends,
I attached my .pdb file in this message, as you see, I have formyl residue in
it. I'd like to get a .gro output of it by using this commands, but getting the
fatal error:
# pdb2gmx -f glc.pdb -o glc.gro -ignh -ter -water spc
Fatal error:
Residue 'FOR' not found in resid
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