I managed to run my simulation but which kind of coulomtype can I use except
PME? also I get different averages for kinetic and potential energies than
before reducing units I think these numbers must be the same because
E*=E/epsilon (epsilon is about 0.9977) for argon. could u please help me
about
trevor brown wrote:
Dear users,
In Gromacs 4.5.3, atom types are defined in
/share/top/oplsaa.ff/atomtypes.atp.
The corresponding bonds for diffrent atopm pairs are described as
between opls_001 and opls_965.
I have a CNT, I need C-C intereaction, which one should I choose?
I would find a
Dear users,
In Gromacs 4.5.3, atom types are defined in
/share/top/oplsaa.ff/atomtypes.atp.
The corresponding bonds for diffrent atopm pairs are described as between
opls_001 and opls_965.
I have a CNT, I need C-C intereaction, which one should I choose?
Second question; where can I find info about
On 15/01/2011 8:50 PM, leila separdar wrote:
I have Gromacs 4.0.7 I have simulated 1000 atoms of Argon with Lenard
Jones potential in a cubic box with linear size of 3.34. but when I
reduced units I confront with this error
Back Off! I just backed up md.log to ./#md.log.5#
Reading file argon.tp
Hi Karbalee,
It says : nanometer squared.
Cheers,
Tsjerk
PS. Many of us are not Justin... :p
On Sat, Jan 15, 2011 at 5:33 PM, shahrbanoo karbalaee
wrote:
> Dear Justin
> Hi,I want to use PCA for compare fluctuations two peptides with 13
> aa. I use this command g_covar
> g_covar #NAME? ru
Dear Justin
Hi,I want to use PCA for compare fluctuations two peptides with 13
aa. I use this command g_covar
g_covar #NAME? run2.tpr#NAME? run2.xtc#NAME?
eigenvaluesbackbone.xvg #NAME? eigenvectorsbackbone.trr#NAME?
covarbackbon.xpm
and get the some of data : ti
mohsen ramezanpour wrote:
I checked this one but it did not solve the problem.
Actually I did in your way and I found the force is very high on one
atom of my ligand,C12.
I checked it's structure with pymol,it 's situation was normal.
can I change it's coordinate a few?
I think it can make fo
I checked this one but it did not solve the problem.
Actually I did in your way and I found the force is very high on one atom of
my ligand,C12.
I checked it's structure with pymol,it 's situation was normal.
can I change it's coordinate a few?
I think it can make force less.
please let me know how
I have Gromacs 4.0.7 I have simulated 1000 atoms of Argon with Lenard Jones
potential in a cubic box with linear size of 3.34. but when I reduced units
I confront with this error
Back Off! I just backed up md.log to ./#md.log.5#
Reading file argon.tpr, VERSION 4.0.7 (single precision)
Back Off! I
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