Hi,
I got this error. Can anyone explain me what it means.
WARNING: This run will generate roughly 10571 Mb of data
starting mdrun 'UNITED ATOM STRUCTURE FOR MOLECULE LIG in water'
1000 steps, 2.0 ps.
NOTE: Turning on dynamic load balancing
DD cell 3 0 0: Neighboring cells do not
Hello everybody,
I have a question about the final conformation after energy minimization. I am
simulating a polymer in vacuo and I used steepest descent method for energy
minimization. When I use an emtol=1000 the structure I get is linear. Then I
tried an emtol=30 because another study about
: [gmx-users] Pressure and box volume
On 3/19/17 8:42 PM, Mishelle Oña wrote:
> Hello Justin!
>
> I was trying to getting down the pressure of my simulation from aprox 300 bar
> to 1 bar. I increased the box volume and now I have 27 bars but my density
> decrease dramatically fro
Hello Justin!
I was trying to getting down the pressure of my simulation from aprox 300 bar
to 1 bar. I increased the box volume and now I have 27 bars but my density
decrease dramatically from 970 to 320 kg/m3. I tried to add more water
molecules to increase it again but then the pressure
unday, March 19, 2017 2:20 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Pressure in NPT simulation
On 3/19/17 3:17 PM, Mishelle Oña wrote:
> Hello,
>
> I have a question concerning pressure. I runned a NPT simulation with the
> following parameters:
>
>
Hello,
I have a question concerning pressure. I runned a NPT simulation with the
following parameters:
; Pressure coupling
Pcoupl = Berendsen
Pcoupltype = Isotropic
tau_p= 1.01325
compressibility = 4.5e-5
ref_p=
rg_gmx-users-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul
<jalem...@vt.edu>
Sent: Saturday, March 18, 2017 8:06 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Pressure problem in EM simulation
On 3/18/17 9:00 PM, Mis
Hello!
I have a question about pressure in EM simulation. I am using Steepest descent
method in a water polymer system. My pressure gets this value:
Energy Average Err.Est. RMSD Tot-Drift
Hello everyone,
I am modifying a force field to simulate a Polymer. I have add the monomers of
my polymer in residuetypes.dat file as follows:
ETHB Polymer
ETHP Polymer
ETHE Polymer
When I run the pdb2gro command a message like this appears:
Processing chain 1 (153 atoms, 30
Hello Gromacs users,
I am searching properties of biopolymers for tissue engineering and one aspect
I am concerned about is crosslinking of polymers in hydrogels. Do any one knows
how to simulate this on Gromacs?
Thank you!
Mishelle
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Gromacs Users mailing list
* Please search the archive
:40 PM, Mishelle Oña wrote:
> Hello
>
> I have a question about energy minimization tool. I am modelling a polymer
> and I use a force field I have developed. I have run a EM and got positive
> values. Can you help me with this?
>
Positive values for what? Are you in vacuo
Hello
I have a question about energy minimization tool. I am modelling a polymer and
I use a force field I have developed. I have run a EM and got positive values.
Can you help me with this?
Best regards,
Mishelle
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Gromacs Users mailing list
* Please search the archive at
Hi,
I am doing some simulations in a cluster. I want to know if there is an option
to run the simulation in order that I can close the terminal?. I tried to make
sbatch but the problem is that when I entered the command there is a step to
choose the system and with sbatch I could not choose
octoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
>
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> o
HiI have a question about calculation of solvation energy using PBSA. From this
approach the G solvation is the sum of the G polar + G nonpolar energy, if I am
calculating the solvation of a nonpolar molecule in water I want to know if iin
this case G polar is 0? Samara
My polimer has total charge 0, you mean that?
Samara
> To: gmx-us...@gromacs.org
> From: jalem...@vt.edu
> Date: Wed, 16 Dec 2015 13:18:48 -0500
> Subject: Re: [gmx-users] PBSA calculations
>
>
>
> On 12/16/15 1:04 PM, Mishelle Oña wrote:
> > HiI have a question
Hi, I am using g_mmpbsa tool for calculate the solvation energy of molecule.
From the paper Kumari et al (2014) g_mmpbsa - A GROMACS tool for
high-throughput MM-PBSA calculations. J. Chem. Inf. Model.54:1951-1962. I
understand that solvation energy is the sum of polar and nonpolar energies so I
Hi, I am using g_mmpbsa tool for calculate the solvation energy of molecule.
From the paper Kumari et al (2014) g_mmpbsa - A GROMACS tool for
high-throughput MM-PBSA calculations. J. Chem. Inf. Model.54:1951-1962. I
understand that solvation energy is the sum of polar and nonpolar energies so I
Hi, I am using g_mmpbsa tool for calculate the solvation energy of molecule.
From the paper Kumari et al (2014) g_mmpbsa - A GROMACS tool for
high-throughput MM-PBSA calculations. J. Chem. Inf. Model.54:1951-1962. I
understand that solvation energy is the sum of polar and nonpolar energies so
Hi, I am using g_mmpbsa tool for calculate the solvation energy of molecule.
From the paper Kumari et al (2014) g_mmpbsa - A GROMACS tool for
high-throughput MM-PBSA calculations. J. Chem. Inf. Model.54:1951-1962. I
understand that solvation energy is the sum of polar and nonpolar energies so I
Hello, I have a question about trjconv. I have a .trr file and I put the
following line of command: trjconv -f trajcentrada.trr -b 1646 -e 1646 -o
1646ps.gro I got back a file of 13813272703 bytes. Then I make the same and got
a file of 506444 bytes. Do you know what is happening?Mishelle
non-trivial trajectories to text
> format.
>
> Mark
>
> On Sun, Nov 15, 2015 at 8:20 PM Mishelle Oña <samimi...@hotmail.com> wrote:
>
> > well, I check and it is the same line of command. The biggest file has
> > more weight than the .traj file and it is onl
e then you can use -dump option.
>
> trjconv -f trajcentrada.trr -dump 1646 -o 1646ps.gro
>
> On Sun, Nov 15, 2015 at 11:39 PM, Mishelle Oña <samimi...@hotmail.com>
> wrote:
>
> > Yes, but I am not converting all the .trr file to gro I wanted to take
> > only one fr
the size of your
> files is worth thinking about, then converting them to gro format is not a
> great idea.
>
> Mark
>
> On Sun, 15 Nov 2015 21:56 Mishelle Oña <samimi...@hotmail.com> wrote:
>
> > Eh, I don´t understand what you mean, please explain me .Mishelle:)
>
Hello,
I have a question about trjconv. I have a .trr file and I put the following
line of command: trjconv -f trajcentrada.trr -b 1646 -e 1646 -o 1646ps.gro I
got back a file of 13813272703 bytes. Then I make the same and got a file of
506444 bytes. Do you know what is happening?
Mishelle
rs] Problems with trjconv
>
> Hi,
>
> Either you didn't issue the same command (inspect your terminal history),
> or the second operation didn't complete (for any number of reasons).
>
> Mark
>
> On Sun, Nov 15, 2015 at 8:13 PM Mishelle Oña <samimi...@hotmail.com>
:06 -0500
> Subject: Re: [gmx-users] Tools for energy of solvation in polimers
>
>
>
> On 11/9/15 8:18 AM, Mishelle Oña wrote:
> > OK I understand, so you think I couldn´t use Gromacs to calculate the
> > Energy of Solvation? If that is the case could you help m
> > To: gmx-us...@gromacs.org
> > From: jalem...@vt.edu
> > Date: Sun, 8 Nov 2015 20:38:18 -0500
> > Subject: Re: [gmx-users] Free solvation, problems with g_bar
> >
> >
> >
> > On 11/8/15 8:35 PM, Mishelle Oña wrote:
> > > Hi everyb
Hi everybody!I am calculating the energy of solvation of a polimer (polilactic
acid.) I have a simulation of 40 000 frames and I am taking random frames of
the simulation to aply the free energy tutorial of gromacs. When I perform the
g_bar tool this messageWARNING: Some of these results
Hi everybody!I am calculating the energy of solvation of a polimer (polilactic
acid.) I have a simulation of 40 000 frames and I am taking random frames of
the simulation to aply the free energy tutorial of gromacs. When I perform the
g_bar tool this message:WARNING: Some of these results
> To: gmx-us...@gromacs.org
> From: jalem...@vt.edu
> Date: Sun, 8 Nov 2015 20:38:18 -0500
> Subject: Re: [gmx-users] Free solvation, problems with g_bar
>
>
>
> On 11/8/15 8:35 PM, Mishelle Oña wrote:
> > Hi everybody!I am calculating the energy of solvation of a pol
Hi!I am simulating a polimer of Polylactic acid with 30 monomers in a water
system. For equilibrate the system I have made NVT, NPT and Process dynamics.
The fiinal dynamic should have 20 000 frames but when I load it in VMD it has
only 12 186 frames. Also the confout.gro file that result from
Hi!I am simulating a polimer of Polylactic acid with 30 monomers in a water
system. For equilibrate the system I have made NVT, NPT and Process dynamics.
The fiinal dynamic should have 40 000 frames but when I load it in VMD it has
only 12 186 frames. Also the confout.gro file that result from
umber of frames
>
>
>
> On 10/29/15 5:46 PM, Mishelle Oña wrote:
> > Hi Justin, Thanks for your reply. I used gmxcheck to verify the trajectory
> > and it didn´t have errors. I got this:
> > Item#frames Timestep (ps)Step 400010.5Time
&g
> Subject: Re: [gmx-users] There is no error message but the dynamic don´t show
> the correct number of frames
>
>
>
> On 10/29/15 6:08 PM, Mishelle Oña wrote:
> > Well, I am trying to calculate the Solvation free energy of my molecule, I
> > am following the Hand
umber of frames
>
>
>
> On 10/29/15 6:21 PM, Mishelle Oña wrote:
> > I attached the .mdp file I usedCould you tell me if there is a better form
> > to
>
> The mailing list does not accept attachments.
>
> > calculate the free energy of my polimer?And how can
the dynamic don´t show
> the correct number of frames
>
>
>
> On 10/29/15 4:50 PM, Mishelle Oña wrote:
> >
> > Hi!I am simulating a polimer of Polylactic acid with 30 monomers in a water
> > system. For equilibrate the system I have made NVT, NPT and Process
> &g
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