; option, which is similar to what Francesca vitalini
> had used:
>
> $MYGROMACSPATH/bin/mdrun -v -s dynamin_dimer_PR1.tpr -o
> dynamin_dimer_PR1.trr -cpo dynamin_dimer_PR1.cpt -c dynamin_dimer_PR1.gro
>
> >From what I understand, the modified version is built to couple the
h for your help
Francesca
2012/6/16 Justin A. Lemkul
>
>
> On 6/16/12 7:54 AM, francesca vitalini wrote:
>
>> yes and I do.
>> By the way the version of GROMACS I'm using is the 3.3.1, I forgot to
>> specify
>> that before.
>>
>>
> OK, I
yes and I do.
By the way the version of GROMACS I'm using is the 3.3.1, I forgot to
specify that before.
2012/6/16 Justin A. Lemkul
>
>
> On 6/16/12 7:41 AM, francesca vitalini wrote:
>
>> Dear Justin,
>>
>> this is my trjcat command
>>
>> /home
have each structure at a different time
step. If I was using it wrongly please correct me.
Thanks in advance for all the help.
Francesca
2012/6/16 Justin A. Lemkul
>
>
> On 6/16/12 6:48 AM, francesca vitalini wrote:
>
>> Dear Gromacs Users,
>>
>> While making a
Dear Gromacs Users,
While making a trajectory connecting different gro files I got the
following output which I don't understand.
Continue writing frames from
/home/cocktail2/vitalini/reverse_transformation_vacuum/300-166-160/300-166-160_annealing.gro
t=1 ps, frame=0
Last frame 0 time
s, and the area of interest is
plotted through xpm2eps only in the lower left corner. How can I manage to
obtain a plot that only focuses on the residues provided by the index file?
I have been searching the mailing list but couldn't find an answer to that.
Thank you in advance.
Best
--
Fra
ntal importance.
Unfortunately I couldn't find any more detailed documentation about it.
Could anyone explain to me what it does or point me to where to find
the related documentation?
Thank you very much
Francesca
2012/3/30 Mark Abraham :
> On 30/03/2012 8:39 AM, francesca vitalini wrote:
>>
, rcoulomb and rvdw to 1. Any ideas
on a faster way to add my position restraints or how to solve the
LINCS error? Thank you very much.
Francesca
2012/3/29 Justin A. Lemkul :
>
>
> francesca vitalini wrote:
>>
>> My minimization was done without any constraints. I'm start
from "all-bonds" to only "h-bonds"
> did the trick for me, although I never exactly figured out why.
> Maybe it's worth a try for you, too?
> Cheers,
> Felix
>
> -Ursprüngliche Nachricht-
> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun
gured out why.
> Maybe it's worth a try for you, too?
> Cheers,
> Felix
>
> -Ursprüngliche Nachricht-
> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im
> Auftrag von francesca vitalini
> Gesendet: Donnerstag, 29. März 2012 15:15
> A
n't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
Francesca Vitalini
PhD student at Computational Molecular Biology Group,
Department of Mathematics and I
I think you can make an index file using make_ndx where you specify
the atoms you want to restraint.
Hope this can help.
Francesca
2012/3/12 James Starlight :
> Dear Gromacs users!
>
>
> I want to perform constrained MD simulation of my protein with inclusion of
> some experimental restraints.
>
>
Either you develop your own version of the mapping or I guess you have
to use the old version...sorry, but I'm struggling with it right now
and I understand that it can be quite problematic.
Francesca
2012/3/9 rama david :
> Dear GROMACS specialists,
> How to convert Coarse Grain Martini
Hello,
I'm trying to do a reverse transformation from coarse grained to all
atom following the MARTINI tutorial and applying it to my system. I
have manually added the dihedral restraint section to my topology and
now, when I try to run the g_fg2cg command I get the following error:
calling cpp...
obtain 2 values more than the input number of quadruplets and I
don't understand why. Is it here something I'm missing from how it
works?
Thanks for any help.
Francesca
2012/2/29 francesca vitalini :
> Thank you. It worked now.
> Best
> Francesca
>
>
>
> 2012/2/29 Mark Ab
Thank you. It worked now.
Best
Francesca
2012/2/29 Mark Abraham :
> On 1/03/2012 1:00 AM, francesca vitalini wrote:
>>
>> Hi Mark,
>> Thanks for your answer. What I'm trying to do is calculate the value
>> in degrees of the angles listed in my index file
. Is there a faster way to get a file that has like two
columns, one for the dihedral and another one for the angles?
Thanks
Francesca
2012/2/29 Mark Abraham :
> On 29/02/2012 11:54 PM, francesca vitalini wrote:
>>
>> 2012/2/29 Mark Abraham:
>>>
>>> On 29/02/201
2012/2/29 Mark Abraham :
> On 29/02/2012 9:39 PM, francesca vitalini wrote:
>>
>> Hi all,
>> I'm trying to use g_angle to calculate a list of dihedrals that I have
>> into an hand made index file (angles.ndx), which looks like
>> [ dihedrals ]
>> 2 5
Hi all,
I'm trying to use g_angle to calculate a list of dihedrals that I have
into an hand made index file (angles.ndx), which looks like
[ dihedrals ]
2 5 9 10
10 15 18 19
.
However it produces a .xvg file where it gives me for each angle in
degrees its probability. However, what I want is in
Hi all,
I'm trying to calculate dihedral angles of a big system using g_angle
and providing an ndx file as input. To create the ndx file I use the a
CA | a C | a N | a CA nomenclature, but I'm not sure if it works for
calculating the omega dihedral of my protein.
Can anyone tell me if I'm doing it
Hi GROMACS community,
I have one problem: I need to calculate the dihedrals for a big system
(so not possible to do it by hand using vmd) starting from a gro file.
Do you know if it exists an efficient way of doing it?
I've seen that the g_chi option exists, however, it doesn't suit for
me as it ca
a lot
2012/1/31 Justin A. Lemkul :
>
>
> francesca vitalini wrote:
>>
>> Well I'm keeping struggling with this script. Apparently the problem in in
>> using the integrator md with the GOMACS 3.3.1 version. In fact the same .mdp
>> file with integrator steep works. w
nks a lot
2012/2/20 Dommert Florian :
> On Mon, 2012-02-20 at 16:05 +0100, francesca vitalini wrote:
>> Just one last question Tsjerk, I was trying to load the cg.gro file
>> obtained with martinize in vmd and the program says it is unable to
>> load the molecule. the resu
90.00 P 1 1
ATOM 1 BB ALA 1 15.063 17.501 13.232 1.00 0.00
ATOM 2 BB GLU 2 14.568 13.732 14.199 1.00 0.00
ATOM 3 SC1 GLU 2 17.373 14.208 15.223 1.00 0.00
TER
ENDMDL
Does it sound right to you?
Thanks
2012/2/20 francesca vitalini
nting
> that out.
>
> By the way, you might want to post these issues on the Martini forum:
> http://md.chem.rug.nl/cgmartini/index.php/user-platform/forum
> It's not exactly Gromacs...
>
> Cheers,
>
> Tsjerk
>
> On Mon, Feb 20, 2012 at 2:34 PM, francesca v
ca,
>
> Given the error, it seems there's still a mismatch between the number
> of atoms and the number indicated. Try converting your structure to
> PDB and use that for coarsegraining.
>
> Cheers,
>
> Tsjerk
>
> On Mon, Feb 20, 2012 at 2:08 PM, francesca
> remove water? In that case you have to update the number of atoms in
> the second line. The error message should be more explanatory though.
>
> Cheers,
>
> Tsjerk
>
> On Mon, Feb 20, 2012 at 1:57 PM, francesca vitalini
> wrote:
>> I was using the one available fr
gt; that the previous version that was available online was one used in a
> workshop, while the script was still in beta.
>
> Cheers,
>
> Tsjerk
>
>
> On Mon, Feb 20, 2012 at 10:43 AM, francesca vitalini
> wrote:
>> Hi all,
>> I'm trying to coarsegrain my stru
Hi all,
I'm trying to coarsegrain my structure using the script martinize.py
and using my gro file as inmput and the dssp file with the second
structure downloaded from http://swift.cmbi.ru.nl/gv/dssp using the
pdb structure as input, I get the following error message that I
really don't understand
Thanks. I was mislead by the syntax in the online reference and forgot
to change everything into bash scripting.
You have been very very helpful!
2012/2/17 Justin A. Lemkul :
>
>
> francesca vitalini wrote:
>>
>> export DSSP /home/cocktail/vitalini/gromacs_special/bin/dssp
export DSSP /home/cocktail/vitalini/gromacs_special/bin/dssp
2012/2/17 Justin A. Lemkul :
>
>
> francesca vitalini wrote:
>>
>> Thanks!
>> However now I jet another error
>> -bash: export: `/home/cocktail/vitalini/gromacs_special/bin/dssp': not
>> a
h the binary file to make it work? n the dssp
website they don't write anything about it.
Thanks again
2012/2/17 Justin A. Lemkul :
>
>
> francesca vitalini wrote:
>>
>> Dear all,
>> In order to get the secondary structure of my pdb file I need to run
>> the do
message:
-bash: setenv: command not found
Any help?
Thanks
--
Francesca Vitalini
PhD student at Computational Molecular Biology Group,
Department of Mathematics and Informatics, FU-Berlin
Arnimallee 6 14195 Berlin
vital...@zedat.fu-berlin.de
francesca.vital...@fu-berlin.de
+49 3083875776
+49
that, any help?
Otherwise, I'm actually just looking for a toy system with which just
play around as I'm having issues with the reverse transformation. Any
suggestion for a pdb? thanks!
--
Francesca Vitalini
PhD student at Computational Molecular Biology Group,
Department of Mathem
012/2/17 Mark Abraham :
> On 17/02/2012 9:14 PM, francesca vitalini wrote:
>>
>> I tried, but apparently the atom that it is looking for exist already
>> in the rtp file!!
>>
>> this is the error
>>
>> Program pdb2gmx, VERSION 3.3.1
>> Source code f
[ dihedrals ]
-CA -C N H1 gd_14
[ impropers ]
-C -O N -CA gi_1
N H H -C gi_1
Any help?
2012/2/16 Justin A. Lemkul :
>
>
> francesca vitalini wrote:
>>
>> Do you mean that I can just use the new version of pdb2gmx than change
>> the included forcefield
sing the GROMACS 3.3.1 version of pdb2gmx I get the aa.top
Trying to reconvert from cg to aa I obtain the message pasted before.
Any ideas?
--
Francesca Vitalini
PhD student at Computational Molecular Biology Group,
Department of Mathematics and Informatics, FU-Berlin
Arnimallee 6 14195 Berli
Do you mean that I can just use the new version of pdb2gmx than change
the included forcefield and in case the name of the atoms and it
should work?
2012/2/16 Justin A. Lemkul :
>
>
> francesca vitalini wrote:
>>
>> Hi all!
>> I'm trying to create a topology fil
ry with 3 atoms
while sorting atoms
---
Any suggestions?
Thanks
--
Francesca Vitalini
PhD student at Computational Molecular Biology Group,
Department of Mathematics and Informatics, FU-Berlin
Arnimallee 6 14195 Berlin
vital...@zed
exactly when Open MPI kills them.
So... How ca I overcome the issue of overlapping atoms?
Thanks
Fra
2012/2/10 francesca vitalini
> In fact in the reverse transformation I'm feeding the CG structure
> information.
> Once I look through VMD to the FG structure I notice that the back
;t think I need
more than energy minimization for that.
What do you think?
2012/2/10 Mark Abraham
> On 11/02/2012 12:41 AM, francesca vitalini wrote:
>
> In order to overcome the problem I tried to fix everything except the
> backbone (solvent, sidechain and CA, as I want the struct
ibrated it yet and I'm keeping it
fixed which could also be a source of overlapping.
Any ideas?
Thanks.
Francesca
2012/2/10 Justin A. Lemkul
>
>
> francesca vitalini wrote:
>
>> I achieve
>>
>> Steepest Descents converged to machine precision in 205 steps,
5496e+07
Maximum force = 2.0486184e+12 on atom 4479
Norm of force = 7.2424045e+13
but again the same issue with table extent and still the production of pdb
files.
Any explanations?
Thanks
Francesca
2012/2/9 Justin A. Lemkul
>
>
> francesca vitalini wrote:
>
>>
Tryed the double precision without any success... Again the same type of
error message. Might need to try other minimization algorithm. Any
suggestions on that?
2012/2/9 Justin A. Lemkul
>
>
> francesca vitalini wrote:
>
>> Hi all!
>> I'm trying to run some ene
000
152461 1000 1000 1000
152471 1000 1000 1000
152481 1000 1000 1000
152491 1000 1000 1000
152501 1000 1000 1000
152511 1000 1000 1000
..
187
Hi all,
I'm sorry for the dumb question but I need to put harmonic restraints on my
peptide and I cannot find the right command. So, looking on the how tos
link in the gromacs website I understand that I need to add to my topology
file a posre.itp file with the section [ distance_restraints ] speci
gt; On 4/02/2012 12:56 AM, francesca vitalini wrote:
>>
>> Yes but those tips are not for bash scripts... :(
>
> You asked how to make the script always use the same no-longer-interactive
> selection. That's the information on the page we linked. The bash loop glue
>
ina
> On Friday 03,February,2012 09:56 PM, francesca vitalini wrote:
>
>> Yes but those tips are not for bash scripts... :(
>>
>
> You'd better post what you have done so far about this script,
>
> probably someone can help you improve or refine it
Yes but those tips are not for bash scripts... :(
2012/2/3 Mark Abraham
> On 4/02/2012 12:21 AM, francesca vitalini wrote:
>
>> Hi!
>> I have to use the gromacs command trjconv to obtain a .gro file from a
>> .xtc and a .pdb file. I have to do it for several files in a
Hi!
I have to use the gromacs command trjconv to obtain a .gro file from a .xtc
and a .pdb file. I have to do it for several files in a bash for loop so
I'd rather prefer to find a way to make my script type in the trjconv
interactive terminal always the same number for the system. Any tips?
Thanks
mtype CH2R not found
any suggestions here?
Thanks
Francesca
2012/1/31 Francesca Vitalini
> Thank you Justin for your quick reply. Unfortunately I cannot use a more
> modern version of GROMACS as my topology and .gro files where first created
> for a reverse transformation from cg
alle ore 14.33, Justin A. Lemkul ha scritto:
>
>
> Francesca Vitalini wrote:
>> Actually the directory is of my own and I have created it in my home
>> directory so that shouldn't be a problem as I also have created other files
>> in the same directory without
ritto:
>
>
> francesca vitalini wrote:
>> Hallo GROMACS users!
>> I'm trying to run a simple md script after running an energy minimization
>> script on my system and I'm getting a wired error message
>> Reading file dynamin_dimer_PR1.tpr, VERSI
Hi!
I posted a message before regarding the reverse transformation with g_fg2cg
command. Now I have managed to re-numerate correctly the residues so that
it doesn't complain about it but I have come across a different problem.
when I run the command it doesn't recognize the ions NA+. So I was
wonde
Hi,
I'm a new GROMACS user and I'm trying to convert a CG file (I have the .top
and .gro for it) to AA using the reverse command g_fg2cg.
Unfortunately I don't have the AA topology file, only the pdb, so I'm
trying to get one using pdb2gmx genbox and genion subsequently. Then I try
to run the g_f
Hi,
I'm a new GROMACS user and I'm trying to convert a CG file (I have the .top
and .gro for it) to AA using the reverse command g_fg2cg.
Unfortunately I don't have the AA topology file, only the pdb, so I'm
trying to get one using pdb2gmx genbox and genion subsequently. Then I try
to run the g_f
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