On 5/06/2012 4:34 PM, Bao Kai wrote:
Hi, all,
I am still trying to do my simulation with liquid mixtures.
I have a simple question now. When I writing my .top file, how could I
know if I should use epsilon-sigma or c6-c12 parameters for the LJ
potential? It seems that in some examples, c6-c12 p
Dear All,
I would like to calculate the dielectric constant of an ice crystal system in a
simulation had about 1 ms.
I used g_dipoles command to do this. The obtained results seemed that they were
only the values of the last frame in the simulation but not the average values,
Dipole moment (De
Hi, all,
I am still trying to do my simulation with liquid mixtures.
I have a simple question now. When I writing my .top file, how could I
know if I should use epsilon-sigma or c6-c12 parameters for the LJ
potential? It seems that in some examples, c6-c12 parameters are used
and epsilon-sigma pa
Dear Gromacs Users,
While dealing with a protein I am facing problem with the
selenomethionins (MSE) residue. I couldn't find the parameters for that
residue. So can anyone suggest me any literature where I can find the OPLS
force-filed parameters for the same ?
Thanks
Regards
T
On 5/06/2012 9:11 AM, Peter C. Lai wrote:
The quick and dirty way is to post-patch Makefile in src/tools.
I think patching the appropriate Makefile.in is sufficient for configure to
pick up and automake into Makefile if all you need to do is append a make
target.
As to your previous question, o
The quick and dirty way is to post-patch Makefile in src/tools.
I think patching the appropriate Makefile.in is sufficient for configure to
pick up and automake into Makefile if all you need to do is append a make
target.
As to your previous question, on our cluster, I use Intel ICC 11.1.056
bo
One more question: How do I get my new g_whatever analysis to be included
in the compilation?
Simply placing my file in src/tools won't work of course. How to I place it
correctly in the build?
Thanks,
-Shay
2012/6/5 Justin A. Lemkul
>
>
> On 6/4/12 5:16 PM, Shay Teaching wrote:
>
>>
>>
>> 2012/
2012/6/5 Justin A. Lemkul
>
>
> On 6/4/12 5:16 PM, Shay Teaching wrote:
>
>>
>>
>> 2012/6/4 Justin A. Lemkul mailto:jalem...@vt.edu>>
>>
>>
>>
>>
>>On 6/4/12 2:59 PM, Shay Teaching wrote:
>>
>>Dear Gromacs users,
>>
>>I want to write new analyses for gromacs and compile it (so
Hi all
I'm trying to simulate a UTP (Uridin Tryphosphate) with charge -4:
O(-) O(-) O(-)
| | |
--O--P--O--P--O--P--O(-)
| | |
O O O
I've used the triphosphate charge parameters published by Oliveira et
al(1). They used the RESP procedure after ca
Dear Peter,
usually I use a simple Makefile like
# Variables set by the configuration script:
GMX_HOME = /home/oteri/PKG/gromacs/4.5.5/gcc/
GMX_SRC = /home/oteri/PKG/sources/gromacs-4.5.5
GSL_HOME = /home/oteri/PKG//gsl/1.15/gcc
MOD_HOME = /home/oteri/PKG/utilities/src
MOD_BIN
On 2012-06-04 05:23:10PM -0400, Justin A. Lemkul wrote:
>
>
> On 6/4/12 5:16 PM, Shay Teaching wrote:
> >
> >
> > 2012/6/4 Justin A. Lemkul mailto:jalem...@vt.edu>>
> >
> >
> >
> > On 6/4/12 2:59 PM, Shay Teaching wrote:
> >
> > Dear Gromacs users,
> >
> > I want to write new
On 6/4/12 5:16 PM, Shay Teaching wrote:
2012/6/4 Justin A. Lemkul mailto:jalem...@vt.edu>>
On 6/4/12 2:59 PM, Shay Teaching wrote:
Dear Gromacs users,
I want to write new analyses for gromacs and compile it (so I'll have
g_whatever) as part of the gromacs pack
2012/6/4 Justin A. Lemkul
>
>
> On 6/4/12 2:59 PM, Shay Teaching wrote:
>
>> Dear Gromacs users,
>>
>> I want to write new analyses for gromacs and compile it (so I'll have
>> g_whatever) as part of the gromacs package.
>> Per the instructions I found on gromacs website, I installed kdevelop and
On 6/4/12 2:59 PM, Shay Teaching wrote:
Dear Gromacs users,
I want to write new analyses for gromacs and compile it (so I'll have
g_whatever) as part of the gromacs package.
Per the instructions I found on gromacs website, I installed kdevelop and opened
the gromacs as a project using kdevelop
On 6/4/12 3:53 PM, John Ladasky wrote:
Recently I have started to get crash messages in my molecular dynamics runs
which look like this:
Reading file exp37b-prep.tpr, VERSION 4.5.4 (single precision)
Making 1D domain decomposition 5 x 1 x 1
starting mdrun 'Protein in water'
50 steps, 1000.
Recently I have started to get crash messages in my molecular dynamics
runs which look like this:
Reading file exp37b-prep.tpr, VERSION 4.5.4 (single precision)
Making 1D domain decomposition 5 x 1 x 1
starting mdrun 'Protein in water'
50 steps, 1000.0 ps.
step 81240: Water molecule start
Dear Gromacs users,
I want to write new analyses for gromacs and compile it (so I'll have
g_whatever) as part of the gromacs package.
Per the instructions I found on gromacs website, I installed kdevelop and
opened the gromacs as a project using kdevelop. However I have two
questions:
1) When I tr
On 5/06/2012 12:08 AM, Laurence Leherte wrote:
Dear Gromacs users,
I am using the Amber99 FF in MD simulations of peptides (and
proteins). In a first stage to the design a different charge
distribution, most of the atomic charges were set equal to zero (i.e.,
all charges but the C and O backb
Dear Gromacs users,
I am using the Amber99 FF in MD simulations of peptides (and proteins).
In a first stage to the design a different charge distribution, most of
the atomic charges were set equal to zero (i.e., all charges but the C
and O backbone atoms).
It appeared that the calculation tim
On 6/4/12 7:29 AM, ramaraju801 wrote:
hi,
i checked the .rtp file residues such as DCN,DC5,DGN,DG5,DAN,DA5,DTN,DT5
dint have any phosphate gp but when i tested the .rtp file with a random DNA
pdb file it is producing a topology file.
Then you'll have to translate this newfound knowledge int
hi,
i checked the .rtp file residues such as DCN,DC5,DGN,DG5,DAN,DA5,DTN,DT5
dint have any phosphate gp but when i tested the .rtp file with a random DNA
pdb file it is producing a topology file.
-ram
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Dear Gromacs Users,
I am trying to study the conformational path from state A to state B with
targeted molecular dynamics. These two states are two different structures
of a peptide that I have calculated after a series of nmr experiments. I
have perform 100ns simulations separately of the two pep
Dear Mark,
What type of file i have to check for missing of atoms.
Thanks and regards.
--
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Dear all gromacs users,
I tried the grompp and i got the following error.
Fatal error:
moleculetype CU1 is redefined.
Is there any explanation why is thid happening?
I've checked [moleculetypes] in topology files and there are not duplicated.
I would appreciate any help. Iam new in using
On 4/06/2012 6:18 PM, Wayne Chen wrote:
Hi,
I'm a student at National Taiwan University doing research on protein-ligand
interactions using MD simulations with GROMACS (version 4.5.3). In our
simulations, we placed a protein (group A) and a ligand (group B) in a box
under periodic boundary condi
Hi,
I'm a student at National Taiwan University doing research on protein-ligand
interactions using MD simulations with GROMACS (version 4.5.3). In our
simulations, we placed a protein (group A) and a ligand (group B) in a box
under periodic boundary condition and ran for 20ns.
I am trying to obt
On 4/06/2012 3:46 AM, ramesh cheerla wrote:
Dear Gromacs experts,
I am planing to use tabulated
potentials for dihedral functional form Summn over 'n' 0.5*K [ ( Cos
n(phi-phi0)] , Here 1<= n <= 3 . I have three different K values (i.e
K1,K2,K3 ) one for eac
On 4/06/2012 5:05 PM, Seera Suryanarayana wrote:
Dear all gromacs users,
While i am running pdb2gmx commond i
am getting following error.
Fatal error:
There were 22 missing atoms in molecule Protein_chain_A, if you want
to use
this incomplete topology.
I w
Dear all gromacs users,
While i am running pdb2gmx commond i am
getting following error.
Fatal error:
There were 22 missing atoms in molecule Protein_chain_A, if you want to use
this incomplete topology.
I wont ignore the 22 missing atoms by using -missing commo
On 4/06/2012 5:00 PM, Acoot Brett wrote:
Dear All,
Will you please tell me how to rename the C-terminal residue atom OXT
so that the OXT oxygen can be recognized by MOLMOL?
You'd have to read the MOLMOL documentation. But start with "O" - making
sure you preserve the file format correctly,
Dear All,
Will you please tell me how to rename the C-terminal residue atom OXT so that
the OXT oxygen can be recognized by MOLMOL?
Cheers,
Acoot--
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