MoJie Duan wrote:
> >So look at your structures like I said last time! I'm not here to give
> >my valuable time giving free advice in order to have it ignored...
>
> Thank you very much for your kindness and patience. Maybe sometimes my
> questions seems to be silly and boring, my knowledge abo
><[EMAIL PROTECTED]><[EMAIL PROTECTED]>So look at your structures like I said last time! I'm not here to give>my valuable time giving free advice in order to have it ignored...Thank you very much for your kindness and patience. Maybe sometimes my questions seems to be silly and boring, my knowledge
See:
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_
residue_topology_database
Catch ya,
Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
[EMAIL PROTECTE
Hi people.
Well, this thread is going to become an independet list for ILs.
We have developed a force field for a small set of cations and anions of
ILs, few year ago, based on AMBER. At the moment, we are (slowly) finalizing
publications on the extension of those for new sets of anions, all
comp
Eudes Fileti wrote:
Dear Mark,
Thank you for the link. It was useful.
I have choosen the volume using the editiconf by setting
the experimental density for toluene. In fact, my potential
can be wrong.
So, I asked you if you would have a topology or an equilibrated box for the
toluene, since this
Osmair Vital de Oliveira wrote:
Dear Mark,
Thank you for the helpful!!. For instance, I have been working with
molecular dynamics simulation using gromacs for five years...
Therefore, my ask is an thoughtful question. Contrary with your
answer..
You didn't technically ask a question :-) In ord
priyanka srivastava wrote:
Dear all,
While running a job, since there was space problem I could not write the
xtc files. Now when I do the analysis and use the trr file it reports
the time values after every 5ps i.e. 2000, 2005, 2010 etc. However I
wish to write the xtc file using trjconv suc
Dear community,
I am trying to separate potential energy contributions coming from the protein
and from water in my solvated protein system.
Dose anybody know if the term, "RF excl" can be computed / written separately
for protein / water atoms? I would be interested in the "RF excl" contribution
Dear community,
Thanks again, Mark! Your comments made me realize that I was mixing two concepts
and allowed me to figure out what was going on. I apologize for the confusion.
The correct formulations are:
a) protein-protein (bonded and non-bonded)
b) protein-solvent (interaction, non-bonded)
c)
Hi!
I am just wondering that why the potential energy couldnt be positive? It must
have been negative after minimization at 0 K, but in the simulation at specific
temperature the energy of the intramolecular interactions increases increasing
the potential energy...
Janne
> Dear Mark,
> Thank you
Dear all,
While running a job, since there was space problem I could not write the xtc
files. Now when I do the analysis and use the trr file it reports the time
values after every 5ps i.e. 2000, 2005, 2010 etc. However I wish to write the
xtc file using trjconv such that the timestep is report
Dear Mark,
Thank you for the helpful!!. For instance, I have been working with
molecular dynamics simulation using gromacs for five years...
Therefore, my ask is an thoughtful question. Contrary with your
answer..
Have a nice day.
On Fri, 17 Aug 2007, Mark Abraham wrote:
> Osmair Vital de Oli
Dear Mark,
Thank you for the link. It was useful.
I have choosen the volume using the editiconf by setting
the experimental density for toluene. In fact, my potential
can be wrong.
So, I asked you if you would have a topology or an equilibrated box for the
toluene, since this could be very useful
Sagittarius wrote:
Dear Gromacs users,
Could you please help me to find out what the problem is.
Curiously enough, pdb2gmx is telling you want the problem is.
I use command
pdb2gmx -f C:\Soft\Gromacs\Input\formaldehyde.pdb -o outputName.gro -p
outputName.top
Fatal error:
Residue 'UNK' not
Sorry, but first I suggest: Read the error message!
Fatal error:
> Residue 'UNK' not found in residue topology database
Now, what could this mean? This actually means, in the forcefield
residue database (e.g. ffoplsaa.rtp) exists no entry for a molecule
named UNK...
Rename the pdb to the expec
MoJie Duan wrote:
> Mark:
> Thank you for your reply!
> I have checked my topology file of the ATP, I think there isn't any
> problem with it. When I do the grompp (only use the ATP molecule), there
> is not any warning and error, it stopped at 14th step, and return the
> following messege:
>
>
Dear Gromacs users,
Could you please help me to find out what the problem is.
I use command
pdb2gmx -f C:\Soft\Gromacs\Input\formaldehyde.pdb -o outputName.gro -p
outputName.top
formaldehyde.pdb looks like this:
COMPNDUNNAMED
Mark:Thank you for your reply!I have checked my topology file of the ATP, I think there isn't any problem with it. When I do the grompp (only use the ATP molecule), there is not any warning and error, it stopped at 14th step, and return the following messege:Step= 0, Dmax= 1.0e-02 nm, Epot= -
Osmair Vital de Oliveira wrote:
Hi,
Somebody has force field parameters of the D-glyceraldehyde-3-phosphate
(GAP).
If you want to ask a question, please ask an thoughtful question. You
should probably also check out
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation and
http://
Eudes Fileti wrote:
Dear Mark, thank you for your reply.
For equilibration of the system, firstly I generated a ordinated lattice
of 10x10x10 molecules.
After, I carried out successive minimization runs (with STEEP and
L-BFGS) up to the system
to reach the convergence for these methods and in
Hi,
Somebody has force field parameters of the D-glyceraldehyde-3-phosphate
(GAP).
Thanks
Osmair
Brazil
_
-
Osmair Vital de Oliveira
Dear GMX developer,
When performing trjconv with gmx3.3.1, it says: "*WARNING no output,
trajectory ended at 100". * When searching mailing list archive, I know that
this is a silly bug and has been fixed in CVS code. The problem is that
when I try to download CVS version with login mode by
Quoting [EMAIL PROTECTED]:
> Hi, everyone:
> I have meet some problem when simulating a protein and ATP complex. The
> energy minimization will stop after 14 steps. I had followed Mark's
> suggestion, did the protein and ATP eneryg minimization independently,
> and found that the protein can fini
Dear Mark, thank you for your reply.
For equilibration of the system, firstly I generated a ordinated lattice of
10x10x10 molecules.
After, I carried out successive minimization runs (with STEEP and L-BFGS) up
to the system
to reach the convergence for these methods and in the sequence I performed
Hi,
thanks for the info! I also found a force field for AMBER.
J. N. Canongia Lopes, J. Deschamps, A. A. H. P$dua, J. Phys. Chem. B.
2004, 108, 2038 –2047.
Sampo
[EMAIL PROTECTED] wrote:
Dear gmx users.
I see that are people in the list asking for ionic liquids parameters.
I have been workin
Dear gmx users.
I see that are people in the list asking for ionic liquids parameters.
I have been working on ionic liquids and I recently published
the parameterization of two ionic liquids ([BMIM][PF6] and [BMIM][NO3])
for the gromos force field using gromacs.
The parameters are published i
Dear Sir,
i wanted to read the source code before doing REMD.
Thanks for your suggestions, i have found that already in the program and in
manual.
Reagrds
-
Once upon a time there was 1 GB storage in your inbox. Click here for happy
ending.
Hi
You have to tell GROMACS in the parameters-file (.ppa) which kind of PMF
you want to calculate (runtype=afm,umbrella). Depending on this choice
it's very likely that the afm_rate is simply ignored for umbrella, no?
The force constant is mimicking the stiffness of the spring. You want to
o
Hi,
I struggled with a similar minimisation problem with NADP (NDPP topology
in ffG43a1). Then I got a suggestion from a colleague in Prof. Ho"ltje's
group in Dusseldorf, that the atom naming should be changed from eg.
AC5* to something with only three characters, eg. C10. I renamed (and
only rena
Thank you for the suggestion !
Originally, there were about 250 residues.
"182 residues" might be from the end-index of
'r_81_r_82_r_83_r_102_r_111_r_149_r_178_r_182' .
Do I make wrong index file ? or, is the result-file normal?
Keunwan Park
Mark Abraham wrote:
> Keunwan Park wrote:
>
>>
[EMAIL PROTECTED] wrote:
> http://www.gromacs.org/pipermail/gmx-users/2007-August/029155.html
>
>
>
> Mark:
> I am sorry to disturb you. I'm a beginner of GROMACS and this
> "mailing-list" system. I even don't know how to replay a post directly.
> And yesterday I haven't seen your replay becau
Hi,
Well, think harder about your 'problem'. How hard can it be to solve
all terms to reach the nearest local minimum for a system of 36 atoms?
You could basically do it by hand! No wonder that you reach
convergence to machine precision in 14 steps. Check the archives on
'stepsize too small' and '
http://www.gromacs.org/pipermail/gmx-users/2007-August/029155.htmlMark:I am sorry to disturb you. I'm a beginner of GROMACS and this "mailing-list" system. I even don't know how to replay a post directly. And yesterday I haven't seen your replay because the list title changed, sorry again!About the
Keunwan Park wrote:
> Dear all
>
> I use index file to make residue group and run g_mdmat function with the
> ndx file.
>
> For example, the residue groups are composed of 8 residues and the
> program said ...
> --
> Selected
Dear all
I use index file to make residue group and run g_mdmat function with the
ndx file.
For example, the residue groups are composed of 8 residues and the
program said ...
--
Selected 10: 'r_81_r_82_r_83_r_102_r_111_r_14
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