Dear all gromacs users,
I tried the "grompp -c 3I40_ion.gro -p 3I40.top -o
3I40_b4em.tpr -f em.mdp" and i got the following error.
Option Filename Type Description
-f em.mdp Input
I guess you have duplicate the "moleculetype" entries for CU1 in your topology
file. Check your topology file again. You can not have more than one
"moleculetype" definition per molecule type.
Cheers,
Emmanuel
=
Emmanuel Birru
PhD
Dear Sir/Madam,
Thanks for the insightful comments from the experts.Follows the steps, I
found the source of error:
This what I have done:
In the following directory
/home/softwares/fftw-3.0.1:./configure --enable-shared
--prefix=/home/sof
On 29/05/2012 6:37 PM, a a wrote:
Dear Sir/Madam,
Thanks for the insightful comments from the experts.Follows the
steps, I found the source of error:
This what I have done:
In the following directory /home/softwares/fftw-3.0.1:
./confi
Hi,
I'm running a number of energy minimizations on a clathrate supercell and I
get quite significantly different values for the total energy depending on
the number of mpi processes / number of threads I use. More specifically,
some numbers I get are:
#cores energy
1-2.4193640920269
Friends,
I read in many articles explaining the behaviour of water in the first (or
second etc) hydration layers around a protein. I am curious to know if
there is any way to obtain/guess the thickness of this layer. How does one
defines the thickness ?
Thanks,
Bala
--
C. Balasubramanian
--
gmx
One option is to calculate the rdf (radial distribution function g_rdf
[-surf]) of water oxygen atoms and find the position of the first few
peaks...
Il 29/05/2012 12:28, Bala subramanian ha scritto:
Friends,
I read in many articles explaining the behaviour of water in the first
(or second et
Ok. My topology:
; Include forcefield parameters
#include "./charmm27.ff/forcefield.itp"
; Include ligand topology
#include "ligand1.itp"
; Include Position restraint file
#ifdef POSRES_1
#include "posre_ligand1.itp"
#endif
; Include ligand topology
#include "ligand2.itp"
; Include Position re
On 5/29/12 6:52 AM, Steven Neumann wrote:
Ok. My topology:
; Include forcefield parameters
#include "./charmm27.ff/forcefield.itp"
; Include ligand topology
#include "ligand1.itp"
; Include Position restraint file
#ifdef POSRES_1
#include "posre_ligand1.itp"
#endif
; Include ligand topology
On Tue, May 29, 2012 at 12:21 PM, Justin A. Lemkul wrote:
>
>
> On 5/29/12 6:52 AM, Steven Neumann wrote:
>
>> Ok. My topology:
>>
>> ; Include forcefield parameters
>> #include "./charmm27.ff/forcefield.itp"
>>
>> ; Include ligand topology
>> #include "ligand1.itp"
>>
>> ; Include Position restr
Hi, all,
I am new to Gromacs and MD. I just went through a few tutorials on
Gromacs quickly. I have a question now.
I know the structure of molecule A and B, such as the atoms
compositions and the relative position of the atoms and the charge.
Now, I want to use 500 A and 100 B to do the simu
On 5/29/12 8:46 AM, Bao Kai wrote:
Hi, all,
I am new to Gromacs and MD. I just went through a few tutorials on
Gromacs quickly. I have a question now.
I know the structure of molecule A and B, such as the atoms
compositions and the relative position of the atoms and the charge.
Now, I wan
On 5/29/12 6:22 AM, Stephen Cox wrote:
Hi,
I'm running a number of energy minimizations on a clathrate supercell and I get
quite significantly different values for the total energy depending on the
number of mpi processes / number of threads I use. More specifically, some
numbers I get are:
#
Dear Mark,
I have overlook it. Sorry.
I have already added the following two sentences in .bashrc file in my home
directory (when I login as user).
export
CPPFLAGS="-I/home/softwares/fftw301/include"
export LDFLAGS="-L/home/softwares/fftw301/lib"
Should I type in anot
Hi, Justin,
Thank you very much for your help.
It seems that genbox will need really huge memory even with thousands
of molecules.
If we want to to further to tens or hundreds of thousands molecules,
do we need some cluster to run genbox in parallel?
Best Regards,
Kai
>
> Message: 3
> Date: T
On 5/29/12 4:19 PM, Bao Kai wrote:
Hi, Justin,
Thank you very much for your help.
It seems that genbox will need really huge memory even with thousands
of molecules.
If we want to to further to tens or hundreds of thousands molecules,
do we need some cluster to run genbox in parallel?
gen
nice suggestioncoletta for ever
PS. Lo so che è un commento inutile, ma qualcosa la devo pur dire :D
2012/5/29 Andrea Coletta
> One option is to calculate the rdf (radial distribution function g_rdf
> [-surf]) of water oxygen atoms and find the position of the first few
> peaks...
On 30/05/2012 1:50 AM, a a wrote:
Dear Mark,
I have overlook it. Sorry.
I have already added the following two sentences in .bashrc file in my
home directory (when I login as user).
export CPPFLAGS="-I/home/softwares/fftw301/include"
export LDFLAGS="-L/home/softwares/fftw301/lib"
Should I
Dear All,
I want to
ask some questions about trajectory analysis. I have some md simulation output
files that includes coordinate, force and velocity information. And these files
are huge ( more than 5 GB ) . Could you please recommend a free text editor
which
works on Linux or Windows to open
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