Dear users,
I wanted to ensure that the option of -pbc in trjconv is only for
visualization,
and if I do all possible calculations with the original .xtc file there wont
be any
problem.
Thank you
With regards
M. Kavyashree
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http://lists.grom
Elisabeth wrote:
Hello Dr. Vitaly Chaban,
Thank you. I asked a friend in our Dept. for help who is working on
different aspects of the more or less similar system. The message below
was sent on behalf of me. I apologize if I should not have done this. We
thought maybe it does not matter und
>
> You had helped me earlier on calculating the heat of vaporization of
> methanol and it worked great. I'm just trying hard to understand
> conceptually what is the difference between simulating a liquid phase
> and a gas phase in Gromacs. I mean technically if we throw in 1000
> molecules of c
Hey Eli:
What is the correlation observed between you and Moeed?
I suppose you eventually compressed your system so much, that it
became very distorted. Check your GRO file. I believe it is not
healthy inside.
Regards.
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Roche
On Thu, 02 Jun 2011 17:20:35 -0400
"Justin A. Lemkul" wrote:
> Fabian Casteblanco wrote:
> > Hi Justin,
> >
> > You had helped me earlier on calculating the heat of vaporization of
> > methanol and it worked great. I'm just trying hard to understand
> > conceptually what is the difference betwee
Mr Bernard Ramos wrote:
Hi everyone!
I have already have the MD data, I need to select certain
atoms/residues with their XYZ coordinates in each time frame. I have
problems in using the g_select if this is the proper tool to use for
this. Thanks.
g_select allows you to create dynamic i
Hi everyone!
I have already have the MD data, I need to select certain atoms/residues with
their XYZ coordinates in each time frame. I have problems in using the g_select
if this is the proper tool to use for this. Thanks. --
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs
Fabian Casteblanco wrote:
Hi Justin,
You had helped me earlier on calculating the heat of vaporization of
methanol and it worked great. I'm just trying hard to understand
conceptually what is the difference between simulating a liquid phase
and a gas phase in Gromacs. I mean technically if w
Hi Justin,
You had helped me earlier on calculating the heat of vaporization of
methanol and it worked great. I'm just trying hard to understand
conceptually what is the difference between simulating a liquid phase
and a gas phase in Gromacs. I mean technically if we throw in 1000
molecules of c
shivangi nangia wrote:
Hello All,
I am trying to solvate a protein sitting in a dodecahedron using genbox.
It gets solvated but a box of solvent is created around the protein.
I want the protein to be sitting in a dodecahedron filed with solvent.
I used the following commands:
editconf -f
Elisabeth wrote:
Dear Justin,
I find:
box (3x3):
box[0]={ 1.6e+01, 0.0e+00, 0.0e+00}
box[1]={ 0.0e+00, 1.6e+01, 0.0e+00}
box[2]={ 0.0e+00, 0.0e+00, 1.6e+01}
box_rel (3x3):
box_rel[0]={ 0.0e+00, 0.0e+00, 0.0e+
Hi,
I am using gromacs_4.0.7 to calculate the Scattering Intensity as a function
of scattering vectors(q) using g_rdf -sq command .
But, I found that there is no way that one can increase/decrease the grid
spacing for structure factor calculation. I tried using -bin option , but that
does not
Dear Justin,
I find:
box (3x3):
box[0]={ 1.6e+01, 0.0e+00, 0.0e+00}
box[1]={ 0.0e+00, 1.6e+01, 0.0e+00}
box[2]={ 0.0e+00, 0.0e+00, 1.6e+01}
box_rel (3x3):
box_rel[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
box_rel[1]
Hello All,
I am trying to solvate a protein sitting in a dodecahedron using genbox.
It gets solvated but a box of solvent is created around the protein.
I want the protein to be sitting in a dodecahedron filed with solvent.
I used the following commands:
editconf -f onlyhis.gro -bt dodecahedro
Elisabeth wrote:
Hello Justin,
Thank you. I am using
gmxdump -s *.tpr -om to produce mdout.mdp file but I dont see box
You don't need an mdout.mdp file, nor would box vectors be present in one. What
you're looking for is the box information present in the .tpr file. Run:
gmxdump -s t
Anna Duncan wrote:
Hi Justin,
Thanks for your speedy response. I've set off the simulation with the
checkpoint file rather than the trajectory and energy files and that
seems to be going fine now.
v4.5.3 g_energy showed the .edr file from the backbone-restrained run to
have no Xi-0-Prot
Hello Justin,
Thank you. I am using
gmxdump -s *.tpr -om to produce mdout.mdp file but I dont see box vector
information. This error happens at the very beginning. I see no steps are
calculated.
On 2 June 2011 13:11, Justin A. Lemkul wrote:
>
>
> Elisabeth wrote:
>
>> Hello all,
>>
>> I am
Thanks Justin. It worked and it is only off by 3% from experimental
value so that is great. Thanks for your help!
--
Best regards,
Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E: fabian.castebla...@gmail.com
--
gmx-users mailing listgmx-use
Hi Justin,
Thanks for your speedy response. I've set off the simulation with the
checkpoint file rather than the trajectory and energy files and that
seems to be going fine now.
v4.5.3 g_energy showed the .edr file from the backbone-restrained run
to have no Xi-0-Protein term present, a
Anna Duncan wrote:
Hi,
I'm doing a coarse-grained simulation, using the MARTINI forcefield, of
a protein in a lipid bilayer. I carried out the equilibration stages
using Gromacs 4.0.7. Equilibration was done in several stages but the
last stage was with a Nosé-Hoover thermostat for tempe
Hi,
I'm doing a coarse-grained simulation, using the MARTINI forcefield,
of a protein in a lipid bilayer. I carried out the equilibration
stages using Gromacs 4.0.7. Equilibration was done in several stages
but the last stage was with a Nosé-Hoover thermostat for temperature
coupling a
Fabian Casteblanco wrote:
Thanks Justin. That clarified a lot. I'm having trouble simulating
the 1 molecule of gas methanol. I took the original energy minimized
molecule and I'm trying to start it off on NVT using the following
*.mdp file. I got rid of PBC (ns_type=simple) and I set
rlist=
Thanks Justin. That clarified a lot. I'm having trouble simulating
the 1 molecule of gas methanol. I took the original energy minimized
molecule and I'm trying to start it off on NVT using the following
*.mdp file. I got rid of PBC (ns_type=simple) and I set
rlist=infinite. After correcting so
Dear community.
Thanks to all, finally I could resolve my problem, with the option
"-setttime", it was vital, then "c" (continue).
Now I have two questions,
1) In which case the option "l" could be useful? I did not understand very
well the aplicability.
2) Could you please recommend me an arti
Nilesh Dhumal wrote:
Hello,
I have a system with a glucose molecule.
I want to calculate the dipole moment of a particular OH in glucose
molecule.I made an index file which have a group containing atoms.
[ O8 ]
8 18
10 is oxygen no. and 20 is hydroen no.
I'm assuming you mean 8 is O
Elisabeth wrote:
Hello all,
I am getting the error below at the very beginning of the simulation
(both serial and parallel). I am sure I did not encounter this problem
before with the same input files. This has just happened now. I really
have no clue why this is happening. could you please
Hello all,
I am getting the error below at the very beginning of the simulation (both
serial and parallel). I am sure I did not encounter this problem before with
the same input files. This has just happened now. I really have no clue why
this is happening. could you please help me? Thank you all
Hello,
I have a system with a glucose molecule.
I want to calculate the dipole moment of a particular OH in glucose
molecule.I made an index file which have a group containing atoms.
[ O8 ]
8 18
10 is oxygen no. and 20 is hydroen no.
But, if I try to use g_dipoles to get the dipole momen
Fabian Casteblanco wrote:
Hello Justin,
Thank you for your response. I just wanted to make sure I understand
what you meant. I'm assuming that you want the one molecule in the
gas phase at its boiling point and you are doing this because you want
the molecule alone with no intermolecular int
Hello Justin,
Thank you for your response. I just wanted to make sure I understand
what you meant. I'm assuming that you want the one molecule in the
gas phase at its boiling point and you are doing this because you want
the molecule alone with no intermolecular interactions? (since heat
of vap
גדעון לפידות wrote:
Hi all,
I have been trying to run a protein ligand simulation in water using
Gromacs version 4.0.7 and GROMOS 53a6 ff. My protein is about 250 aa and
my ligand is pip3 (Phosphatidylinositol (3,4,5)-trisphosphate) which I
have constructed using PRODRG (using EM and full ch
Hi all,
I have been trying to run a protein ligand simulation in water using Gromacs
version 4.0.7 and GROMOS 53a6 ff. My protein is about 250 aa and my ligand
is pip3 (Phosphatidylinositol (3,4,5)-trisphosphate) which I have
constructed using PRODRG (using EM and full charges option). I have tried
shivangi nangia wrote:
Dear gmx-users,
I was carrying out a continuation of an NPT equilibration from NVT.
As soon the job started it ran into the following error:
Fatal error:
Not enough memory. Failed to realloc 1488624 bytes for nl->shift,
nl->shift=0x0
(called from file ns.c, line 101)
Dear gmx-users,
I was carrying out a continuation of an NPT equilibration from NVT.
As soon the job started it ran into the following error:
Fatal error:
Not enough memory. Failed to realloc 1488624 bytes for nl->shift,
nl->shift=0x0
(called from file ns.c, line 101)
What is the error about?
LinkedIn
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--
Chinmay,
I'd like to add you to my professional network on LinkedIn.
- srajan
Accept invitation from srajan jain
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Fabian Casteblanco wrote:
Hello all,
I am trying to find the enthalpy of vaporization for 7 types of
alcohols to try to compare to experimental values. I have all of them
simulated to equilibrium and I can use g_energy to view the Total
Energy (both kinetic and potential). In order for me to
Hello all,
I am trying to find the enthalpy of vaporization for 7 types of
alcohols to try to compare to experimental values. I have all of them
simulated to equilibrium and I can use g_energy to view the Total
Energy (both kinetic and potential). In order for me to find the
enthalpy of vaporiza
On Wed, 2011-06-01 at 23:37 +0200, Thomas Koller wrote:
> Hello,
>
> I calculate the viscosity with g_energy using option -vis (Gromacs
> 4.0.7):
>
> g_energy -f file.trr -s file.tpr -vis visc.xvg
>
> Why do I get viscosity values only until the half of the simulation
> time?
This results f
On 2/06/2011 5:52 PM, Anirban Ghosh wrote:
Hi ALL,
I am using in calculating the distribution of a solvent around the COM
of a protein chain using g_rdf. When I plot the output file (attached)
I get a curve which increases first (from 1 to a value of about 2.5)
and then decreases to x-axis valu
Hi ALL,
I am using in calculating the distribution of a solvent around the COM of a
protein chain using g_rdf. When I plot the output file (attached) I get a
curve which increases first (from 1 to a value of about 2.5) and then
decreases to x-axis values ranging from 1 to 5. If I understand correc
The error message already shows some hints. Try recompile FFTW with -fPIC.
Jianguo
From: Chandan Choudhury
To: gmx-users
Sent: Thursday, 2 June 2011 15:03:03
Subject: [gmx-users] gmx4.5.4 installation help
Hello gmx-users,
I am trying to install gmx-4.5.4
On 2/06/2011 5:03 PM, Chandan Choudhury wrote:
Hello gmx-users,
I am trying to install gmx-4.5.4 on a HPC Linux cluster x86_64.
1. I installed fftw 3.2.2
./configure --prefix /soft/sudip/abc/execs/fftw/
--enable-single --enable-threads
2. Installing Gromacs : CPPFLAGS and LDFLAGS
Hello gmx-users,
I am trying to install gmx-4.5.4 on a HPC Linux cluster x86_64.
1. I installed fftw 3.2.2
./configure --prefix /soft/sudip/abc/execs/fftw/
--enable-single --enable-threads
2. Installing Gromacs : CPPFLAGS and LDFLAGS were written in bashrc file
a) ./config
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