.@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Re: boundaries in PMF
>
>
>
> On 5/31/12 3:37 PM, Rebeca García Fandiño wrote:
> > Hi,
> > the center of mass of my channel is at the middle of the ion channel, and
> > it is
> > a symmetric sy
Thu, 31 May 2012 15:52:48 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Re: boundaries in PMF
>
>
>
> On 5/31/12 3:51 PM, Rebeca García Fandiño wrote:
> > OK,
> > however, just one point about your last comment:
> >
> &
Hi,
the center of mass of my channel is at the middle of the ion channel, and it is
a symmetric system, so I suppose these results would be OK. Anyway, I will
check the options you propose.
Thanks a lot for all your comments!!
Best wishes,
Rebeca.
> Date: Thu, 31 May 2012 20:08:26 +0200
> From:
your help.
Best wishes,
Rebeca.
> Date: Thu, 31 May 2012 13:45:18 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] boundaries in PMF
>
>
>
> On 5/31/12 1:38 PM, Rebeca García Fandiño wrote:
> > Thanks a lot for your quick answer.
&
l^-1 nm^-2
pull_nstxout= 1000 ; every 2 ps
pull_nstfout= 1000 ; every 2 ps
> Date: Thu, 31 May 2012 13:25:26 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] boundaries in PMF
>
>
>
> On 5/31/12 1:20 PM, Rebeca G
Hi,
I am trying to calculate a PMF for an ion along a channel. Everything went OK,
but when I used g_wham I got a profile with strange dimensions for the x-axis.
What are the boundaries g_wham is using for calculating the units of x-axis?
I have used:
g_wham -it tpr-files.dat -if pullf-files.dat
Hi,
I am trying to simulate a nanotube inserted into a lipid bilayer using Gromacs
4, applying an external electric field (in the direction of the z axis).
I have added this line to my input file:
;Electric field
E_z = 1 1.0 0
The calculations finish without problem, however I can
size, should it?
Rebeca.
> Date: Sun, 11 Sep 2011 17:39:55 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] analysis of PMF calculations
>
>
>
> Rebeca García Fandiño wrote:
> > Thanks again, I have uploaded to the version 4.5.4 an
help.
Best wishes,
Rebeca.
> Date: Sun, 11 Sep 2011 16:33:54 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] analysis of PMF calculations
>
>
>
> Rebeca García Fandiño wrote:
> > Hi,
> > thanks a lot for your quick
t: Re: [gmx-users] analysis of PMF calculations
>
>
>
> Justin A. Lemkul wrote:
> >
> >
> > Rebeca García Fandiño wrote:
> >> Hello,
> >> I have some old calculations (Umbrella Sampling) carried with Gromacs
> >> 3.3.3 and I would like to
Hello,
I have some old calculations (Umbrella Sampling) carried with Gromacs 3.3.3
and I would like to analyze them using Gromacs 4.
When I use:
/GROMACS/4.5/32/bin/g_wham -bins 100 -temp 300 -tol 0.0001 -min -2.4750
-max 2.4750 -o pmf_1_cycl.xvg -hist histogram_cycl.xvg -ip
./pdo-files.dat
Thanks a lot for your quick answer!
Best wishes,
Rebeca.
> Date: Wed, 10 Aug 2011 14:34:42 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] append files in Gromacs 3.3
>
>
>
> Rebeca García Fandiño wrote:
> > Hello,
&g
Hello,
I have some old calculations (Umbrella Sampling) carried with Gromacs 3.3.3 and
I need to extend them.
I have tried to use the option "append" like in Gromacs 4.0, using:
mdrun -v -np 8 -s Cl-2.4750_b.tpr -pi Cl-2.4750.ppa -po pullout.ppa -pn
Cl-2.4750.ndx -pd -deffnm Cl-2.4750 -append
Hello,
some days ago you had recomended me to use a dodecahedron box and "pull_dim = Y
Y Y" to try to decrease some error bars I was obtaining in my PMF calculations
(trying to calculate the binding energy of two cyclic peptides).
Now, I have run these calaculations, but I have a doubt for the
I have used a cubic box of dimensions 8 x 8 x 14 (nm), and my total pulling was
5nm along the z direction. I dont´t think there could be a problem with the
PBC, since the layer of solvent around the protein is quite big, although I
suppose that using a dodecahedron box for this system would hav
Thu, 21 Jul 2011 15:16:52 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: FW: [gmx-users] large error bars in PMF
>
>
>
> Rebeca García Fandiño wrote:
> >
> >
> > I am trying to achieve the binding energy of the dimer composed
.
Best wishes,
Rebeca.
> Date: Thu, 21 Jul 2011 15:16:52 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: FW: [gmx-users] large error bars in PMF
>
>
>
> Rebeca García Fandiño wrote:
> >
> >
> > I am trying to achieve the b
; pmfs aligned on the long distance value and not on the "minimum" which
> is
> probably what you did ... if the minimum is not well defined then it
> does not
> make sense.
>
> On Jul 21, 2011, at 1:36 PM, Justin A. Lemkul wrote:
>
> >
> &g
a lot again for your help.
Best wishes,
Rebeca.
> Date: Thu, 21 Jul 2011 15:16:52 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: FW: [gmx-users] large error bars in PMF
>
>
>
> Rebeca García Fandiño wrote:
> >
> >
> > I am t
jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] large error bars in PMF
>
>
>
> Rebeca García Fandiño wrote:
> > Hi,
> > thanks a lot for your quick answer.
> > What I am trying to pull are two small peptides one from another (r_1
> &
Hi,
thanks a lot for your quick answer.
What I am trying to pull are two small peptides one from another (r_1 and r_2).
I did not understand very well your last suggestion: "...if you want reasonable
error bars you will not lots of well-converged data".
Do you mean I will need also more windows
Hi,
I am trying to calculate the binding energy of two molecules using the PMF
(Umbrella Sampling method) and Gromacs 4.0.
Some weeks ago I have written to the list because changing the number of
windows used in the Umbrella Sampling calculations different results were
obtained, and I was
Hello,
I am trying to extend a PMF calculation (Umbrella Sampling calculation). In
first place I used tpbconv:
tpbconv -s umbrella_3.tpr -o umbrella_3b.tpr -extend 1000
And then I run it using mdrun:
mdrun -s umbrella_3b.tpr -cpi umbrella_3.cpt -pf pullf-umbrella_3.xvg -px
pullx-umbrella_3.x
for pullf*.xvg and pullx*.xvg and then join them for the analysis?
Best wishes,
Rebeca.
> Date: Tue, 12 Jul 2011 17:59:44 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] number of windows in PMF
>
>
>
> Justin A. Lemkul wrote:
>
or generating more windows?
Thanks a lot again for your help.
Best wishes,
Rebeca.
> Date: Tue, 12 Jul 2011 16:53:54 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] number of windows in PMF
>
>
>
> Rebeca García Fandiño wrote:
>
Hello,
I am trying to calculate the binding energy between two monomers in three
different dimers, using PMF (Umbrella Sampling method) and following Justin's
tutorial.
Using 100 windows separated 0.05 nm I get the PMFs represented in
"pmf_using_100_points.pdf" (attached), and using 50 windows
ct: Re: [gmx-users] restraints in PMF (Justin's tutorial)
>
>
>
> Rebeca García Fandiño wrote:
> > Thanks a lot for your quick answer!
> > I think they are separated enough, however my monomers are cyclic (like
> > discs); I start with a parallel conform
Subject: Re: [gmx-users] restraints in PMF (Justin's tutorial)
>
>
>
> Rebeca García Fandiño wrote:
> > Hello,
> > I am trying to obtain the PMF from Umbrella Sampling of the process of
> > separating two monomers of a dimer, following Justin 's t
Date: Mon, 20 Jun 2011 17:03:56 -0400
> From: jalem...@vt.edu
> To: rega...@hotmail.com
> CC: gmx-users@gromacs.org
> Subject: Re: doubt about your Umbrella Sampling tutorial
>
>
>
> Rebeca García Fandiño wrote:
> > Dear Justin,
> > my name is Rebe
Hello,
I am trying to obtain the PMF from Umbrella Sampling of the process of
separating two monomers of a dimer.
I am following the tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html
and I have a doubt:
In this tutorial the generation of config
Hello,
I am trying to calculate the diffusion coefficient of a molecule in water using
g_msd, and I have a doubt:
I get 3 different values when I use the trajectory directly from the
simulation, the trajectory using PBC conditions, and the "fitted trajectory".
Which would be the correct value fo
Thanks a lot for the clarification, now it works perfectly. Sorry for the
confusion!
Best wishes,
Rebeca.
> Date: Fri, 14 Jan 2011 13:46:26 -0500
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] g_analyze with multiple sets
>
>
>
> Reb
Hello,
I have several files containing two columns, x and y (x is the same for all of
them).
I would like to calculate the average and standar deviation (as the error bar)
for the y column for all my data sets.
I have tried using g_analyze:
g_analyze -n 3 -av average.xvg -errbar stddev -f set1.
OK,
you are right, I haven´t noticed the -z option!
I will try it.
Thanks a lot for your help.
Best wishes,
Rebeca.
> Date: Thu, 16 Dec 2010 15:34:05 -0500
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] g_bundle question
>
>
>
> Reb
z axis of the membrane, am I right?
Thanks a lot for your help.
Best wishes,
Rebeca.
> Date: Thu, 16 Dec 2010 11:59:38 -0500
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] g_bundle question
>
>
>
> Rebeca García Fandiño wrote:
>
Hello,
I am trying to calculate the tilt angle of the principal axis of a nanotube
inserted into a membrane using g_bundle. In the index file I have selected a
group of atoms at the top and a group of atoms at the bottom of the nanotube,
and I using the option -na 1 and -z to calculate the tilt
Hello,
I am trying to calculate the Ramachandran plot for a molecules based on
non-standar aminoacids, parametrized with the Gaff force field and simulated
with Gromacs 4.0.7.
When I try using g_rama -f trajectory.xtc -s topology.tpr -o rama.xvy
I get: Found 0 phi-psi combinations.
I suppose
Hello,
I have an old trajectory simulated using the Charmm force field and I would
like to get the Phi/Psi dihedral combinations as a function of time, using
g_raman. I am using a single pdb to start with.
I created a topology for this pdb using:
pdb2gmx -f protein.pdb -o protein_gmx.pdb -p top
Hi,
I am trying to get the topology of a cyclic peptide, but when I try to
do pdb2pgx I get automatically the correction to a terminal one.
I have looked in the Gromacs list and I only have found a entry about
it,
http://osdir.com/ml/science.biology.gromacs.user/2006-08/msg00297.html
but I
ctory, I can provide that as well.
>
> -Justin
>
> >
> > Thanks,
> >
> > Berk
> >
> > > Date: Tue, 23 Feb 2010 13:51:39 -0500
> > > From: jalem...@vt.edu
> > > To: gmx-users@gromacs.org
> > > Subject: Re: [gmx-user
Hi,
thank you very much for your answer. However, I have tried with the 4.0.7
version, and the problem continues, and it is just the same. I have the
trajectory and tpr file obtained with the 4.0.4 version. Do you think it cares,
or maybe is it another problem?
Cheers,
Rebeca.
From: g...@hotma
Hi,
I am trying to calculate g_rdf using only the x and y components of the
distance (gromacs 4.0.4):
g_rdf -f trajectory.xtc -s production1.tpr -n index.ndx -o rdf_Na_xy.xvg -com
-norm -pbc -xy and the calculations stays at the window:
Select a group: 1
Selected 1: 'UNK'
Select a group: 4
Sel
Hi,
I would like to calculate the density maps for the water inside a pore that has
a cilindrical shape, but not the water outside it, that is also present in the
box.
I don´t understand vey well the options of g_densmap "-amax" and "-rmax". With
-amax I define the maximun axial distance from
Feb 11, 2010, at 7:40 PM, Rebeca García Fandiño wrote:Hi,
I am doing PMF calculations using Gromacs 3.3.3, and I have found very
different results using 2 different machines. Attached you can see that the
graphics are really different for both cases (about 10 KJ/mol!!). The version
of Gromacs
Hi,
I am doing PMF calculations using Gromacs 3.3.3, and I have found very
different results using 2 different machines. Attached you can see that the
graphics are really different for both cases (about 10 KJ/mol!!). The version
of Gromacs (3.3.3) and number of processors used (2) is the same fo
Hi,
I would like to calculate the PMF of an ion along a channel using Gromacs 4,
and I have a doubt about the options I should use in the .mdp file:
-which option should I choose for pull_geometry: distance? direction? or
position?
-which is the equivalent option to the old "Pos1" (in Gr
Hi,
I am trying to calculate the PMF of an ion with Gromacs 4. I have read in the
Gromacs list that the pull code had been completely rewritten in the new
version of Gromacs, but I cannot find much information about the new way to use
this.
Reading the manual (pag 280) I can see: “The option
Hi,
I am trying to calculate the PMF of an ion with Gromacs 4. I have read in the
Gromacs list that the pull code had been completely rewritten in the new
version of Gromacs, but I cannot find much information about the new way to use
this.
Reading the manual (pag 280) I can see: “The options -
Hi,
I am trying to simulate an organic system which has a planar-square Pt center.
To mantain the planar geometry of the metal, I have thought about 2
possibilities:
-introduce 2 dummy atoms at the axial possitions of the metal; however, I get
errors complaining about these extra atoms has mas
Hi,
I am trying to simulate an organic system which has a planar-square Pt center.
I am following the methodology employed in JACS 2008, 10040 (where they use
amber calculations). There, they use 2 dummy atoms to mantain the planar square
geometry of the metal.
I have built my system with no
Hello,
I have done a simulation using Gromacs 4 (4.0.2) and I would like to have a
trajectory were the protein is fitted to the first structure (to mantain the
exact orientation).
When I have tried
echo 1 1 0 | trjconv -f production_1_3.xtc -s production1.tpr -center -fit
rot+trans -pbc mol -
Thank you very much, Alan.
In this case, I am not using acpypi, since I am using a topology for dopc
already published, and it is already converted into Gromacs. So, it´s
manually, as you suppose. I will follow your suggestion and change c and o by
c_ and o_.
Best wishes,
Rebeca.
From:
Hi,
I am doing a simulation combining amber and Gaff force field (for dopc lipids),
this is the first part of my topology file:
; UNK_GMX.top created by acpypi on Thu Jun 4 22:06:03 2009
[ defaults ]
; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ
1 2
Hi,
I am trying to simulate a system using the parameters for ions developed by
Joung et al. and implemented in Amber (frcmod.ionsjc_spce).
I have the topology and the crd file. Now, I want to obtain the topology for
Gromacs using amb2gmx.pl, so I must change the default parameters (for tip3p)
anyway, if want to try the Aqvist's parameters take a look
> inside ffoplsaa.atp file (opls_408 for K+).
>
> best regards,
>
> André
>
> > Rebeca García Fandiño wrote:
> >>
> >> Thank you very much, André. Could you please indicate me how could
>
;
> >> Date: Mon, 1 Jun 2009 19:34:27 +0200
> >> From: sp...@xray.bmc.uu.se
> >> To: gmx-users@gromacs.org
> >> Subject: Re: [gmx-users] crystals of KCl during simulation
> >>
> >> Rebeca García Fandiño wrote:
> >> > Thank you very
Yes, I use PME.
> Date: Mon, 1 Jun 2009 19:34:27 +0200
> From: sp...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] crystals of KCl during simulation
>
> Rebeca García Fandiño wrote:
> > Thank you very much for your answer. I have read some rec
Thank you very much for your answer. I have read some recent literature, and
you are right, it is a problem about the parameters for ions in Amber.
I have found this paper:
Parameters of Monovalent Ions in the Amber-99 Forcefield: Assesment of
Inaccuracies and Proposed Improvements
http://
Hi,
I am trying to simulate a protein in aqueous solution 1M (KCl) with Gromacs and
using the amber force field.
I get the topology of the solvated protein - without the ions- from amber
(Leap) and then used the script amb2gmx.pl to obtain the Gromacs .top and .gro
files.
I did not introduced
Re: [gmx-users] bond, angle and dihedral restraints in Gromacs
>
>
>
> Rebeca García Fandiño wrote:
> > Hello,
> > I would like to simulate a CNT and I want to apply a harmonic potential:
> > -on the C-C bonds
> > -on the bond angles
> > -on the dihedral angles
>
Hello,
I would like to simulate a CNT and I want to apply a harmonic potential:
-on the C-C bonds
-on the bond angles
-on the dihedral angles
with a different spring constant for each case.
I have read Section 4.3 from Gromacs manual, but I actually have some doubts
about how to include this i
Hello,
I am trying to do a -rerun simulation in Gromacs 4.0.4 to calculate the
interaction energy between 2 residues using the trajectory I already had from
the previous simulation:
/gpfs/apps/GROMACS/4.0.4/bin/mdrun -v -deffnm E_interaccion_Asp -dlb auto
-rerun equilibrado3_19.xtc
Hello,
I have a problem in extending a MD simulation in Gromacs.
When I use 32 processors for the calculation, everything goes OK. The
simulation finishes well and I can extend it with tpbconv.
However, I would like to increase the number of processors used up to 64.
Using the same options for
Hello,
I am trying to do Replica Exchange with 50 replicas, but I am having problems
when using trjcat with -demux.
trjcat -f mdA_0.xtc mdA_1.xtc mdA_2.xtc mdA_3.xtc mdA_4.xtc mdA_5.xtc mdA_6.xtc
mdA_7.xtc mdA_8.xtc mdA_9.xtc mdA_10.xtc mdA_11.xtc mdA_12.xtc mdA_13.xtc
mdA_14.xtc mdA_15.xtc m
Hello,
I am trying to do Replica Exchange with 50 replicas, but I am having problems
when using trjcat with -demux.
trjcat -f mdA_0.xtc mdA_1.xtc mdA_2.xtc mdA_3.xtc mdA_4.xtc mdA_5.xtc mdA_6.xtc
mdA_7.xtc mdA_8.xtc mdA_9.xtc mdA_10.xtc mdA_11.xtc mdA_12.xtc mdA_13.xtc
mdA_14.xtc mdA_15.xtc m
Hello,
I am trying to joing different .xtc fragments of a gromacs trajectory using
trjcat (Gromacs 4.0.2 version).
trjcat_sp -f file1.xtc file2.xtc -o join1_2.xtc
I get the following error:
(...)
Reading frame 1 time 22202.002Summary of files and start times used:
Fil
Hello,
I am trying to do REMD for a protein unfolding. I am following the information
given in http://wiki.gromacs.org/index.php/REMD but I am completely new in
these type of simulations. I would like to ask two questions to more advanced
users. I hope you could help me:
-I have seen that the
.uu.se> To: gmx-users@gromacs.org> Subject: Re: [gmx-users] Urea
topology problem> > Rebeca García Fandiño wrote:> > Hello,> > I don´t
understand the correction I should do from itp.> > I have removed from the urea
original urea.itp these lines,> > don't
entific de Barcelona rega...@hotmail.com
> Date: Thu, 18 Dec 2008 09:21:41 -0500> From: jalem...@vt.edu> To:
> gmx-users@gromacs.org> Subject: Re: [gmx-users] Urea topology problem> > > >
> Rebeca García Fandiño wrote:> > > > > > > ERROR 1 [file solv
Hello,
I would like to simulate a proteína in urea, using Gromacs. I have tried to use
the box included in Gromacs by default (urea+h2o.gro and urea.itp).
The topology of the urea/water-solvated protein is:
; Include forcefield parameters
#include "ffG43a2.itp"
#include "protein.itp"
; In
real area of each layer.
Could anybody suggest how could I calculate this paremeter in this type of
simulations?
Thank you very much in advance.
Rebeca García Fandiño
Parc Cientific de Barcelona
[EMAIL PROTECTED]
_
Prueba los
program?
Thank you very much for your help in advance,
Rebeca García Fandiño
Parc Cientific of Barcelona
_
¿Preparándote para el verano? En Windows Live Search encontrarás las mejores
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http
ew version, and I only change fourier_nx and
fourier_ny in the input .mdp file, would it be enough to create a correct
mdp.out file that works.
Best wishes,
Rebeca García Fandiño
Parc Cientific de Barcelona
From: [EMAIL PROTECTED]: [EMAIL PROTECTED]: RE: [gmx-users] invalid number of
---
When I had tried the same with 256 proc, using fourier_nx= fourier_ny=512, the
correspondent error did not appear.
Is there a limit of processors in Gromacs for grompp or which could be the
problem?
Thank you very much for your help in advance,
Rebeca García Fandiño
Parc Cientific of
.
Anybody knows what could be happening?
Thank you very much in advance,
Rebeca García Fandiño
Parc Cientific of Barcelona
_
¿Preparándote para el verano? En Windows Live Search encontrarás las mejores
dietas para conseguir tu
Hello,
I am trying to equilibrate a protein+membrane system in Gromacs 4. The
minimization went OK, but in the equilibration at constant pressure I got this
error:
Fatal error:1 particles communicated to PME node 3 are more than a cell length
out of the domain decomposition cell of their ch
Hello,
I am trying to simulate a protein that has 2 chains (in a membrane, but the
problem is in the protein). One of the chains of the protein has 416 residues
and the other 421. I want to simulate it using the amber force field, so I have
prepared the topology for each one of them and then co
d the lipid properties of that distribution, then I might
change my mind. > > Chris.> > -- original message --> > Rebeca García Fandiño
wrote:> > > > Hello,> > > I would like to simulate a membrane + protein system
using the OPLS > > > force fiel
Hello,
I would like to simulate a membrane + protein system using the OPLS force field
for both, the protein and the membrane. I have looked for a previous
equilibrated membrane simulated using the OPLS force field, but I did not find
it.
Please, does anybody knows where I could find a membrane
any idea to solve this?
Thank you very much for your help in advance.
Rebeca García Fandiño
Parc Cientific de Barcelona
[EMAIL PROTECTED]
_
Sigue en directo todas las competiciones deportivas en MSN Deportes
http
tr outside of string at ./amb2gmx.pl line 212, line 1.
Is there a way to transform amber systems to gromacs in spite of the “*”
symbols? Has anyone transformed this type of systems? How could I save the
problem?
Thank you very much for your help in advance,
Rebe
Hello,
I am new in Gromacs, and I am trying to simulate the interaction between a DOPC
membrane and a protein.
I have equilibrated my system at constant volume and now I would like to switch
to constant pressure.
I think the best option for me is to use ANISOTROPIC pressure, because I want
to s
Hello,
I am a new user of Gromacs, and I am trying to simulate a system of a membrane
composed by POPC, cholesterol and sphingomyelin and a protein. I am using
lipid.itp, but it includes ffgmx.itp, and I have read it is deprecated, so I am
having a lot of problems to introduce the protein to
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