Dear gromacs users,
I want to simulate small molecule - choline which is not neutral, it has
uncompensated positive charge. When I transform mol2 file to pdb structure
looks distorted (not correct) in VMD. I added with genion to the system a
negative ions, but the pdb structure is still distorted.
On 30/03/2011 7:50 PM, Olga Ivchenko wrote:
Dear gromacs users,
I want to simulate small molecule - choline which is not neutral, it
has uncompensated positive charge. When I transform mol2 file to pdb
structure looks distorted (not correct) in VMD. I added with genion to
the system a negativ
On 30/03/2011 5:58 PM, Terry wrote:
Hi, all,
I have four trajectories which I want to analyze Surface on. So I run
for i in 1 2 3 4; do echo -e " non-Water \n Protein " | g_sas -f $i.xtc -s
$i.tpr -o $i.area.xvg -n index.ndx -q $i.pdb ; done
But the strange thing is, g_sas analyzed the first
Dear Friends,
Right now i am working on the docking of a small ligand to a receptor. in order
to begin md simulations in gromacs, i need to create some files..
I have already docked my ligand to the receptor and i have those files:
- ligand_receptor.gro
- posre.itp (for only the receptor
On 30/03/2011 8:14 PM, Ghassen Hassani wrote:
Dear Friends,
Right now i am working on the docking of a small ligand to a receptor.
in order to begin md simulations in gromacs, i need to create some files..
I have already docked my ligand to the receptor and i have those files:
- ligand_rec
Hi Mark,
The output is like this:
WARNING: masses and atomic (Van der Waals) radii will be determined
based on residue and atom names. These numbers can deviate
from the correct mass and radius of the atom type.
2565 out of 4931 atoms were classified as hydrophobic
Back Off! I
Hi Justin,
I checked carefully. The make command also gave the same error as pasted
below. How should I deal this error?
at' follow
.libs/libxdrf.o:libxdrf.c:(.text+0x31e3): undefined reference to `_xdr_int'
.libs/libxdrf.o:libxdrf.c:(.text+0x340b): undefined reference to `_xdr_int'
.libs/libxdrf
Monisha Hajra wrote:
Hi Justin,
I checked carefully. The make command also gave the same error as pasted
below. How should I deal this error?
For Windows systems, Gromacs needs to use internal XDR definitions (rather than
those that are available system-wide on most Unix/Linux machines).
On 30/03/2011 9:21 PM, Terry wrote:
Hi Mark,
The output is like this:
WARNING: masses and atomic (Van der Waals) radii will be determined
based on residue and atom names. These numbers can deviate
from the correct mass and radius of the atom type.
2565 out of 4931 atoms were
Dear gromacs users,
I am planning to produce C-C rdf for my system and I have difficulty making
the index file with a group of all C in the system, [Carbon] . .If there are
thousands of atoms in the system do I have to go through the top file and
note down C atom numbers and use those numbers to m
Elisabeth wrote:
Dear gromacs users,
I am planning to produce C-C rdf for my system and I have difficulty
making the index file with a group of all C in the system, [Carbon] .
.If there are thousands of atoms in the system do I have to go through
the top file and note down C atom numbers an
Dear all,
I asked this question a few days ago but did not receive a solid answer. Has
anyone tried to produce the properties below? Can you comment on accuracy of
these properties using g_energy?
Thermal expansion coeff. (NPT): Enthalpy, Vol, Temp
Isothermal compressibility: Vo
Hi
I am trying to do a QM/MM calculation with gromacs/CPMD. When I try to use a
parallel version of mdrun and CPMD I get a segmentation fault.
I have seen in the examples that LAM is used in runcpmd. It is mandatory for
parallel runs?
Thanks
***
Elena
ETH Zürich an
Hello,
I am trying to calculate the dipole moment autocorrelation
function for my system (ionic liquid). I am using gromacs 4.0.7 version.
I run the simulation for 4 ns. I run the following command to calculate
the dipole moment autocorrelation function
g_dipoles -f water.trr -s water.tpr -co
Hi,
I need to calculate a running average on pressure, and have problem in using
the -ravg option in g_energy command:
I have tried the followings:
1. g_energy -f file.edr -ravg ravg.xvg -o pressure.xvg
2. g_energy -f file.edr -ravg -o pressure.xvg
I could get the fluctuations in pressure.xvg, b
On 2011-03-30 18.54, Nilesh Dhumal wrote:
Hello,
I am trying to calculate the dipole moment autocorrelation
function for my system (ionic liquid). I am using gromacs 4.0.7 version.
I run the simulation for 4 ns. I run the following command to calculate
the dipole moment autocorrelation funct
simon sham wrote:
Hi,
I need to calculate a running average on pressure, and have problem in
using the -ravg option in g_energy command:
I have tried the followings:
1. g_energy -f file.edr -ravg ravg.xvg -o pressure.xvg
2. g_energy -f file.edr -ravg -o pressure.xvg
I could get the fluctuat
Thanks.
How can I take average.
How much long I should run the simulation.
Nilesh
On Wed, March 30, 2011 12:59 pm, David van der Spoel wrote:
> On 2011-03-30 18.54, Nilesh Dhumal wrote:
>
>> Hello,
>>
>>
>> I am trying to calculate the dipole moment autocorrelation
>> function for my system (ion
Dear all,
Dear Justin,
This time I want to ask the gurus about this problem I encountered in
the Equilibration step of my system made of 3 individual (small) protein
chains in a solvated DMPC bilayer, no ions present since the protein
system is neutral...
Following the tutorial I started wit
On 2011-03-30 20.16, Nilesh Dhumal wrote:
Thanks.
How can I take average.
summing up and dividing by the number of sims.
How much long I should run the simulation.
until the average converges.
Nilesh
On Wed, March 30, 2011 12:59 pm, David van der Spoel wrote:
On 2011-03-30 18.54, Nilesh D
Dr. Ramón Garduño-Juárez wrote:
Dear all,
Dear Justin,
This time I want to ask the gurus about this problem I encountered in
the Equilibration step of my system made of 3 individual (small) protein
chains in a solvated DMPC bilayer, no ions present since the protein
system is neutral...
F
Dear all,
I intend to obtain vaporization heat per volume for a *pure alkane system*.
Here is the steps I am taking. Please correct me.
1- Obtain total energy of system (kinetic+potential) and divide by number of
molecules to obtain energy per mol of molecules. g_energy -f *.edr -nmol XXX
2- Obta
On 2011-03-30 21.22, Elisabeth wrote:
Dear all,
I intend to obtain vaporization heat per volume for a /pure alkane
system/. Here is the steps I am taking. Please correct me.
1- Obtain total energy of system (kinetic+potential) and divide by
number of molecules to obtain energy per mol of molec
Elisabeth wrote:
Dear all,
I intend to obtain vaporization heat per volume for a /pure alkane
system/. Here is the steps I am taking. Please correct me.
1- Obtain total energy of system (kinetic+potential) and divide by
number of molecules to obtain energy per mol of molecules. g_energy -
Dear Users and Developers
I am trying to execute md_pull.mdp {given below} on a small molecule
embedded at the core of lipid bilayer. I have tried to modify the
md_pull.mdp from the Tutorial by Justin Lemkul on Umbrella sampling.
I encounter LINCS warning (1000) after about 100-110 ps of
raghu...@bcpindia.org wrote:
Dear Users and Developers
I am trying to execute md_pull.mdp {given below} on a small molecule
embedded at the core of lipid bilayer. I have tried to modify the
md_pull.mdp from the Tutorial by Justin Lemkul on Umbrella sampling. I
encounter LINCS warning (10
Dear users,
Before energy minimization step , I performed the preprosessing step using
grompp .
However, there are two note that :
*NOTE 1 [file topol.top, line 52]:*
System has non-zero total charge: -1.50e+01
*NOTE 2 [file topol.top]:*
The largest charge group contains 11 atoms.
Sinc
Hi Ahmet,
As suggested, it's better to break up your molecule into smaller
charge groups. Note that charge groups don't need to have zero charge,
nor integer charge. In your case, I'd suggest two COH groups for EDO,
which will have zero net charge each, and for TRS I'd take the COH
groups as separ
On 31/03/2011 5:18 PM, ahmet y?ld?r?m wrote:
Dear users,
Before energy minimization step , I performed the preprosessing step
using grompp .
However, there are two note that :
*_NOTE 1 [file topol.top, line 52]:_*
System has non-zero total charge: -1.50e+01
This is an integer. See
ht
,
Regards,
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Date: Wed, 30 Mar 2011 21:31:22 +0200
From: David van der Spoel
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