Steve Fiedler wrote:
Gromacs Users:
While porting field parameters to Gromacs, I ran across unexpected
electrostatic energies returned by the ewald summation method. To
simplify the problem, I reduced the system to two partially charged
particles. For the simplest case of only one box, n =
Mark Abraham wrote:
Luca Mollica wrote:
Dear users,
I am experiencing some troubles in using GMX 4.0.4 trying to rerun
trajectories and obtaining energies for single residues and/or portion
of proteins. According to the mdrun command help and to my experience
with the previous versions of GR
Hi,
Actually I am not confused regarding the clustering method that is being used
in default. I
know that the method that is used is "Single linkage " method.
I got to know the options that I had used in my "g_cluster" command after going
through
g_cluster -h.
Regarding the command "g_cluster
Respectable Justin/Mark
For the study of diffusion of oxygen in water, I tried to search the itp file
for oxygen molecule but could not find. Therefore, I have tried to make it
myself.
Please tell me whether it is fine.
[ moleculetype ]
; molname nrexcl
OMOL 1 ; as there are two atoms in an o
To whom it may concern，
when I used g_saltbr to compute some salt bridges in my system, I
couldn't understand the option "-t". The tutorial tell me that it's trunc
distance and the default is 1000. Then I want to find the definition of the
salt bridge in Gromacs. However, I couldn't fi
ilayer
>
> [ molecules ]
> ; Compound#mols
> Protein_A 1
> Protein_B 1
> DMPC 128
>
> but when I gave this topology file to grompp it shws error-
> no. of coordinates in coordinate file doesn,t mach the topology file .
>
> Can yo
Dear all,
I am interested to calculate the hydrophobic and hydrophilic area of the
surface of the protein layer I am simulating. It looked like g_sas would be
able to give me what I was looking for. But I was wondering what the
difference is between the calculation group and the output group.
Hi Nitu,
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of gmx-users digest..."
Please!...
And don't include the whole digest.
>
> Dear Mark
> Thanks for your reply. as u ask- how many atoms is--Protein A- 5244
>
> protein B- 4658
>
Cheong Wee Loong, Daniel wrote:
Dear all,
I am interested to calculate the hydrophobic and hydrophilic area of the
surface of the protein layer I am simulating. It looked like g_sas
would be able to give me what I was looking for. But I was wondering
what the difference is between the
Dear Mark
Thanks for your consideration.
I am replying you again I think it will be more easy for u in understanding
my problem.
as u ask- how many atoms is--Protein A- 5244
Protein B- 4658
And in one dmpc molecule there is 46 atoms so
Sunil Thapa wrote:
Respectable Justin/Mark
For the study of diffusion of oxygen in water, I tried to search the itp
file for oxygen molecule but could not find. Therefore, I have tried to
make it myself.
Please tell me whether it is fine.
[ moleculetype ]
; molname nrexcl
OMOL 1 ; as the
mary wrote:
>
>
> To whom it may concern，
>
> when I used g_saltbr to compute some salt bridges in my system, I
> couldn't understand the option "-t". The tutorial tell me that it's
> trunc distance and the default is 1000. Then I want to find the
> definition of the salt bridge in Gr
nitu sharma wrote:
Dear Mark
Thanks for your consideration.
I am replying you again I think it will be more easy for u in
understanding my problem.
as u ask- how many atoms is--Protein A- 5244
Protein B- 4658
And in one dmpc molecul
sarbani chattopadhyay wrote:
Hi,
Actually I am not confused regarding the clustering method that is being
used in default. I
know that the method that is used is "Single linkage " method.
I got to know the options that I had used in my "g_cluster" command
after going through
g_cluster -h.
R
Hello All,
I have managed to get urea into the G53a6 ffield with suitable
adjustments to the appropriate .pdb, .rtp, and .hdb files. I am trying
to use the resulting urea.gro file (I have also tried with a urea.pdb
file generated from the urea.gro file using pdb2gmx) in genbox using
the -
Which version of Gromacs? There was a bug in genbox that was fixed for version
4.0.4.
-Justin
Ken Rotondi wrote:
Hello All,
I have managed to get urea into the G53a6 ffield with suitable
adjustments to the appropriate .pdb, .rtp, and .hdb files. I am trying
to use the resulting urea.gro
Sorry, vers 4.0.4 here on an intel macbook running OSX.5.5
On Apr 23, 2009, at 11:06 AM, Justin A. Lemkul wrote:
Which version of Gromacs? There was a bug in genbox that was fixed
for version 4.0.4.
-Justin
Ken Rotondi wrote:
Hello All,
I have managed to get urea into the G53a6 ffield w
Ken Rotondi wrote:
Sorry, vers 4.0.4 here on an intel macbook running OSX.5.5
Does it work if you use -ci to insert your molecule, then in a separate step,
use -cs to solvate?
-Justin
On Apr 23, 2009, at 11:06 AM, Justin A. Lemkul wrote:
Which version of Gromacs? There was a bug in
Dear Justin, All,
Yes, running as two separate steps works, is this a known genbox bug?
Ken
-works-
pdb2gmx -f diala.pdb -o diala.gro -p diala.top -ff G53a6 -ignh
editconf -f diala.gro -o dialabox.gro -bt dodecahedron -box 3.1
genbox -cp dialabox.gro -ci urea.gro -nmol 1 -o dialaurea.gro -p
Ken Rotondi wrote:
Dear Justin, All,
Yes, running as two separate steps works, is this a known genbox bug?
I don't know that it's a bug per se, more of a limitation. The program is
trying to solvate the structure, as well as cram in X molecules of something
else all at once and probably
Indeed this seems likely. I was able to add 125 urea and solvate w/out
incident doing it in two steps.
Thanks again,
Ken
On Apr 23, 2009, at 1:31 PM, Justin A. Lemkul wrote:
Ken Rotondi wrote:
Dear Justin, All,
Yes, running as two separate steps works, is this a known genbox bug?
I don
Dear gmx-user
I am a very new user in gromacs. I encounter the problem with coarse-grained
option in gromacs.
I have installed the option from the MARTINI tutorials which is
“gromacs_reverse.tar.gz”.
It is ok with following the tutorial to do the coarse-graining but when I
want to do all atomi
Dear Ladies and Gentlemen,
I from the University of Applied Sciences in Mittweida currently
deals with the calculation of a propene molecule using the program
Gromacs.
For testing proposer I tried to generate my own force field.
However, when creating the top-file with this command "grompp_d -f pr
??? ? wrote:
Dear gmx-user
I am a very new user in gromacs. I encounter the problem with
coarse-grained option in gromacs.
I have installed the option from the MARTINI tutorials which is
“gromacs_reverse.tar.gz”.
It is ok with following the tutorial to do the coarse-graining but
Saskia Frenzel wrote:
Dear Ladies and Gentlemen,
I from the University of Applied Sciences in Mittweida currently
deals with the calculation of a propene molecule using the program
Gromacs.
For testing proposer I tried to generate my own force field.
However, when creating the top-file with this
Thanks Justin for the reply. I did read the help and manual and understand
that the output file can be the whole or part of the calculation group. What I
don't quite understand is what the output group represents. I am assuming that
the calculation group would be the group of atoms that will b
Cheong Wee Loong, Daniel wrote:
Thanks Justin for the reply. I did read the help and manual and understand
that the output file can be the whole or part of the calculation group. What
I don't quite understand is what the output group represents. I am assuming
that the calculation group would
Thanks for the explanation. It is much clearer now. Although I still don't
quite understand why we can't just use Protein A as the calculation group AND
output group to find the SASA of protein A. I know it states that the
calculation group should be all non-solvent atoms, but I guess I am ju
Cheong Wee Loong, Daniel wrote:
Thanks for the explanation. It is much clearer now. Although I still don't
quite understand why we can't just use Protein A as the calculation group AND
output group to find the SASA of protein A. I know it states that the
calculation group should be all non-s
To whom it may concern，
when I used g_saltbr to compute some salt bridges in my system, I
couldn't understand the option "-t". The tutorial tell me that it's trunc
distance and the default is 1000. Then I want to find the definition of the
salt bridge in Gromacs. However, I couldn't f
xiongxuqiong wrote:
To whom it may concern，
when I used g_saltbr to compute some salt bridges in my system, I
couldn't understand the option "-t". The tutorial tell me that it's
trunc distance and the default is 1000. Then I want to find the
definition of the salt bridge in Gromacs
Justin A. Lemkul wrote:
From g_saltbr -h:
"A minimum distance can be given, (eg. the cut-off), then groups that
are never closer than that distance will not be plotted."
Basically, if a salt bridge occurs within the truncation distance
specified by -t, it will be plotted. Using the defau
Ah ok. Fair enough. Thanks!
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Justin A. Lemkul
Sent: Friday, April 24, 2009 10:48 AM
To: Gromacs Users' List
Subject: Re: [gmx-users] g_sas
Cheong Wee Loong, Daniel wrote:
> Than
Cheong Wee Loong, Daniel wrote:
Thanks for the explanation. It is much clearer now. Although I
still don't quite understand why we can't just use Protein A as the
calculation group AND output group to find the SASA of protein A.
If A is complexed to B in solvent you might want the true SASA o
Dear MARK
Now the problem of matching of topology file and
coordinate file solved but the other two errors come during running grompp
in the second step of inflategro .
my command line is like this- grompp -f em.mdp -p topolinflate.top -c
inflated_system.gro -o inflated-em.tp
Both of those errors are telling you want you need to do. In your
topol_A.itp file, there are no parameters for a particular proper
dihedral. So, define one. Same with the next message. And it even
tells you which line the issue is on in the .itp file, so very easy to
track down which bonds are
nitu sharma wrote:
Dear MARK
Now the problem of matching of topology file and
coordinate file solved but the other two errors come during running
grompp in the second step of inflategro .
my command line is like this- grompp -f em.mdp -p topolinflate.top -c
inflated_syst
Hi,
Of course you can. But if part of Protein A is buried in an interface,
doing the SAS calculation over A only will also include the surface
interface; it will give the total surface of A. That may actually be
handy if you want to determine what the buried surface is. You
calculate the total sur
Hi all. Thanks for all your replies. I think I understand it now and can
definitely see how having the calculation and output group would add to the
flexibility and utilty of g_sas.
Thanks.
Daniel
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@grom
39 matches
Mail list logo
