regards,
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Uppsala Universitet - Sweden
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But it is not quite happening simultaneously, Justin.
It is producing one after another and, consequently, backing up the files.
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:
are you sure that your binary is parallel?
how many frames do those trajectory files contain?
Dr. Vitaly V. Chaban
On Sun, Feb 23, 2014 at 5:32 PM, Marcelo Depólo marcelodep...@gmail.com
wrote:
Maybe I should explain it better.
I am using *mpirun -np 24 mdrun -s prt.tpr -e prt.edr -o
the .mdp files were copied
from a sucessful folder.
But thank you both for the support.
2014-02-23 20:20 GMT+01:00 Mark Abraham mark.j.abra...@gmail.com:
On Sun, Feb 23, 2014 at 6:48 PM, Marcelo Depólo marcelodep...@gmail.com
wrote:
Justin, the other runs with the very same binary do
have incorrect parallelism in this case.
Can you post all the files you obtain for people to inspect?
Dr. Vitaly V. Chaban
On Sun, Feb 23, 2014 at 9:04 PM, Marcelo Depólo marcelodep...@gmail.com
wrote:
Justin, as far as I realized, the next log file starts at 0ps what would
mean
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Hi guys!
Consider the atoms 1, 2 and 3 forming a triangle: I was wondering how can I
calculate the barycenter of this triangle using the atoms coordinates?
I want to measure the distance through time but I am not sure if there is a
simple way to do it.
Cheers!
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Biochemicist
...@gromacs.org.
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Biochemicist
University of Viçosa - Brazil
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the protocol that you have
used. Just the production mdp file will not provide enough info to say
anything. Please send your protocol and mdp files.
Cheers!
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Marcelo Depólo Polêto
Student of MSc Cell and Molecular Biology - UFRGS (Brazil)
B.Sc. Biochemistry - University of Viçosa (Brazil
files, so as your force field that you
have choose. It is hard to say anything without more details.
Also, what do you mean by 'unwinding'? Could you be more specific?
Thank you in advance for your suggestions.
best regards
Urszula
Cheers!
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B.Sc. Biochemistry
2015-03-20 14:21 GMT-03:00 Justin Lemkul jalem...@vt.edu:
On 3/20/15 1:16 PM, Marcelo Depólo wrote:
As my previous email said: there is a modified GROMOS forcefield for
carbohydrated. Install it and check out which kind of modifications on
topologies you should do.
Install it, sure
There is also a Modified GROMOS forcefield for glycans here:
http://dx.doi.org/10.1021/ct300479h
Cheers!
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Student of MSc Cell and Molecular Biology - UFRGS (Brazil)
B.Sc. Biochemistry - University of Viçosa (Brazil)
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Thanks for the insights, Mark.
It was a 'aprun' issue. When I remove it from the command, everything
worked out.
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2015-03-13 14:10 GMT-03:00 Mark Abraham mark.j.abra...@gmail.com:
On Fri, Mar 13, 2015 at 5:46 PM, Marcelo Depólo marcelodep...@gmail.com
wrote:
Hey,
I have
python and
genbox?
Does anyone has a suggestion?
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B.Sc. Biochemistry - University of Viçosa (Brazil)
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Hi,
I've done an extensively search out the web but I could not find LJ
parameters for Fluoride (ionic). Gromos54A7 has only Fluorine parameters.
Does anyone knows any new parameters for that?
Best regards!
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Marcelo Depólo Polêto
Student of MSc Cell and Molecular Biology - UFRGS (Brazil
Hi guys!
Is there a maximum value of Force Constant for Position restraints? Reading
the Manual I could only find the default and the equation to describe it.
Best,
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Marcelo Depólo Polêto
Group of Structural Bioinformatics - Center of Biotechnology
Student of MSc Cell and Molecular Biology
.
The coefficient is four because of the Nyquist theorem. I believe GMX
tests for high vibrational frequencies according to 20*pi*tau on the left
(ten times the period).
Hope this helps.
Alex
On Tue, Apr 21, 2015 at 1:02 PM, Marcelo Depólo marcelodep...@gmail.com
wrote:
Hi
this as an error.
Would someone knows a neat way to do this?
Cheers!
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Student of MSc Cell and Molecular Biology - UFRGS (Brazil)
B.Sc. Biochemistry - University of Viçosa (Brazil)
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Nope! They are just for our amusement.
Maybe only one has to do it: Check your input! David van der Spoel
Cheers!
Marcelo Depólo
Em 13/04/2015 07:05, Priya Das priyadas...@gmail.com escreveu:
Dear All,
*gcq#6: It's So Lonely When You Don't Even Know Yourself (Red Hot Chili
Peppers
, MD 21201
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Student of MSc Cell and Molecular Biology - UFRGS (Brazil)
B.Sc. Biochemistry - University of Viçosa (Brazil)
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2015-04-14 14:54 GMT-03:00 Justin Lemkul jalem...@vt.edu:
On 4/14/15 1:48 PM, Marcelo Depólo wrote:
Hi!
I was wondering if there is any clear way to create position restraints
for
ions. I am using:
*g_select -s rna_ions.gro -n index.ndx -on rna_ion.ndx -select 'group
non-Water
2015-04-14 17:26 GMT-03:00 Justin Lemkul jalem...@vt.edu
On 4/14/15 3:25 PM, Marcelo Depólo wrote:
*Fatal error:[ file rna_ion.itp, line 1753 ]:Atom index (90849) in
position_restraints out of bounds (1-1748).This probably means that you
have inserted topology section
Em 05/04/2015 14:44, Jashimuddin Ashraf jashimuddin.ashra...@gmail.com
escreveu:
Dear gromacs users,
I am trying to simulate liquid SO2 (Sulphur dioxide). So I tried to create
an equilibrated structure of SO2 molecules using the gmx insert-molecules
function. As I try to minimize the energy
-05 1.5129e-08
H1 0.000 0.000 A 0 0
Best regards,
--
Marcelo Depólo Polêto
Group of Structural Bioinformatics - Center of Biotechnology
Student of MSc Cell and Molecular Biology - UFRGS (Brazil)
B.Sc. Biochemistry - University of Viçosa (Brazil
14000 elementsGroup
2 (ANI) has 14000 elementsSelect a group:
0---Program g_dos_506,
VERSION 5.0.6Fatal error:Index contains atom numbers larger than the
topology*
Does anyone have an idea about it?
Cheers!
--
Marcelo Depólo Polêto
Em 22/07/2015 14:51, Christopher Neale chris.ne...@alum.utoronto.ca
escreveu:
Dear Users:
I believe that gromacs 5 pdb2gmx does not faithfully reproduce the
AMBER99sb-ILDN force field.
It is not exclusive behavior for any particular FF. I've got same error for
Gromos54a7. If one uses multiple
!
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Group of Structural Bioinformatics - Center of Biotechnology
Student of MSc Cell and Molecular Biology - UFRGS (Brazil)
B.Sc. Biochemistry - University of Viçosa (Brazil)
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acs Users mailing list
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> > posting!
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2015-08-25 17:29 GMT-03:00 David van der Spoel sp...@xray.bmc.uu.se:
On 25/08/15 18:24, Marcelo Depólo wrote:
Hi all!
I've been running gmx dos (version 5.0.4) in some trajectories with the
following:
echo BEN | gmx_504 dos -s ben.DOS.tpr -f ben.DOS.trr -g ben.log -dos
dos.xvg -vacf
polyelectronic biomolecules (nucleic acids and membranes),
widely reported.
I would check this cases before designing any simulation
Cheers,
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Marcelo Depólo Polêto
Structural Bioinformatics Group
Master Student - BCM/UFRGS
B.Sc. Biochemistry - UFV
Em 13/09/2015 09:42, "Vitaly V. Chaban" <vvcha
re
> posting!
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M
of what each of these types mean?
Thanks in advance!
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DSc. Cell and Molecular Biology - UFRGS (Brazil)
Group of Structural Bioinformatics - Room 202
Center of Biotechnology - UFRGS
Phone: + 55 51 3308-7770
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he h-bonds donated by H atom and accepted by the O atom
at the same time? If so, is there anyway to calculate both separately?
Cheers!
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DSc. Cell and Molecular Biology - UFRGS (Brazil)
Group of Structural Bioinformatics - Room 202
Center of Biotechnology - UFRGS
Phone: + 55 51
; I would use the selection groups judiciously, for example have one of them
> with only donor atoms in it.
>
> Mark
>
>
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Marcelo Depólo Polêto
DSc. Cell and Molecular Biology - UFRGS (Brazil)
Group of Structural Bioinformatics - Room 202
Center of Biotechnology - UFRGS
Phone
Thanks, Justin!
It worked just fine.
I guess using a flag to include different atomtypes into the analyses would
be a nice feature for next GROMACS versions.
Cheers!
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Marcelo Depólo Polêto
DSc. Cell and Molecular Biology - UFRGS (Brazil)
Group of Structural Bioinformatics - Room 202
Center
Hi,
Can gmx hbond also calculates hbonds between non-canonical atoms like S or
F as well? If so, how can I do it?
Cheers!
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Hi
Can someone explain what does each column on atomname2types.n2t mean?
For gromos53a5 it is:
H H0.408 1.008 1 O 0.1
O OA -0.674 15.9994 2 C 0.14 H 0.1
C CH3 0.000 15.0351 C 0.15
C CH0 0.266 12.0114 C 0.15 C 0.15 C 0.15
Hi,
I had the same struggle benchmarking a similar system last week. Just for
curiosity, could you tell us the performance you get when sharing your GPU
with multiple jobs?
In my case (6k atoms + Reaction field + 8 cores 2.2Ghz + TitanX Pascal),
I've got ~440 ns/day. However, I get ~280 ns/day
Hi!
I am running ACF calculations in gmx hbond tool in 5.0.7 version.
When running:
gmx hbond -s mol.tpr -f mol.xtc -tu ns -b 0 -e 10 -ac acf_0-10ns.xvg
and
gmx hbond -s mol.tpr -f mol.xtc -b 0 -e 1 -ac acf_0-10ns.xvg
The results given for the ACF are completely different (example:
Hi,
I am not sure how to interpret the cos(theta1) around my reference atom.
The help printed is not straightforward when comes to set which atoms forms
the angle theta1. For instance.
"theta_1: the angle with the vector from the first atom of the solvent
molecule
to the midpoint between atoms
Hi everyone!
I was wondering about the cmaptypes format within cmap.itp file.
[ cmaptypes ]
C N CT C N 1 24 24\
I understand that C-N-CT-C = phi, N-CT-C-N = psi and 24x24 is the grid
size. What does this '1' mean?
Thanks in advance!
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Postdoctoral Researcher
BIOAGRO
Hi all,
I've been investigating the implementation of CMAP in GROMACS and, as far
as I understood, the current CMAP format does not allow the use of
residue-specific CMAPS, since it is based on atomtypes and not on function
numbers, as GROMACS normally do.
For example, for AMBER, the function
3129
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r that its
"y-axis" would be PSI and "x-axis" would be PHI?
Cheers!
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Postdoctoral Researcher
BIOAGRO - Room T07
Department of General Biology - UFV
Contact: + 55 31 3612-2464
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