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
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
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
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
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
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
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
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
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.
&
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:
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:
> >
> &
.@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
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
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:
>
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:
>
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
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
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
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
> &
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
; 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
.
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
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
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
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
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
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 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
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
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
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
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 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
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
>
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
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://
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
;
> >> 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
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
>
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)
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
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:
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 -
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
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
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
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 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
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:
>
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
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.
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
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 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 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 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
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 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
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,
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
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
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
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
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
.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
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
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 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 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 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
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
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
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
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
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 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
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
.
Anybody knows what could be happening?
Thank you very much in advance,
Rebeca García Fandiño
Parc Cientific of Barcelona
_
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dietas para conseguir tu
---
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
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
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
dietas para conseguir tu peso ideal
http
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
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