Dear users,
I found MARTINI CG force fields.
http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html
On Thu, Sep 4, 2008 at 3:14 PM, Xavier Periole <[EMAIL PROTECTED]> wrote:
> On Thu, 4 Sep 2008 14:59:55 -0400
> "Myunggi Yi" <[EMAIL PROTECTED]> wrote:
>
>> Dear gmx users,
>>
>> I'd like to r
AS> The system works now, thanks for finding a simple mistake. Another question I had is if I want to calculate the average velocities of all the atoms over a period of time can I use g_traj to create an average velocity of the atoms, but looking at all_veloc.xvg file the atom number starts a
Hi,
how does it count the drift in g_energy? What is the equation? What is the
difference among fluct. and RMSD? Thanks, see you soon.
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Please search the
Thank you.
Sorry for not being clearer. I meant where in the source code are the energy
related functions & variables?
Omer.
Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
On Thu, Sep 4, 2008 at 16:19, Jochen Hub <[EMAIL PROTECTED]> wrot
Manoj Kumar Singh wrote:
What if I want to restrain distance between two different molecules. I
tried this and getting error. I looked at some previous posts and didn't
find any solution to this. Some of them say it is limitation of Gromacs.
Since distance restraints are added to the topol
On Sat, 06 Sep 2008 06:13:35 -0400
"Justin A. Lemkul" <[EMAIL PROTECTED]> wrote:
Manoj Kumar Singh wrote:
What if I want to restrain distance between two different molecules. I
tried this and getting error. I looked at some previous posts and didn't
find any solution to this. Some of them s
On Sat, 6 Sep 2008 04:59:54 -0400
"Myunggi Yi" <[EMAIL PROTECTED]> wrote:
Dear users,
I found MARTINI CG force fields.
That is the best choice you could make! :))
http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html
Then dig a bit in the website and you'll find everything to start a
simula
Hi,
RMSD is your just deviation of backbone from native stare while RMS fluctuation
shows the
per atom deviation throughout simulation.
regards,
Ravi Datta Sharma Lecturer, Bioinformatics,
Department of Microbiology,
CCS Unversity,
Meerut
Hello,
Where can I read about the exact format of the TRR and XTC files. I
mean the width and type of every field in the binary trajectory file.
I see read_'next_frame(status,&fr)' function in 'template.c'. But
where is this fuction defined?
Sorry, I'm not an expert in C. :(
Thanks.
--
Vitaly
Vitaly Chaban wrote:
Hello,
Where can I read about the exact format of the TRR and XTC files. I
mean the width and type of every field in the binary trajectory file.
I see read_'next_frame(status,&fr)' function in 'template.c'. But
where is this fuction defined?
Sorry, I'm not an expert in C. :
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