Dear Justin
My final .xtc rmsd graph starts about 4 nm and after
some steps it falls down to 0.3 and quickly goes up again, totally it is
tossing around a straight line near 4 nm, what did I do wrong? As mentioned
in my previous mail about centering of protein inside the box, the gro file was
Dear Justin and Tsjerk
you said Some tools handle PBC properly, some don't .
I want to know exactly which tools of gromacs handle PBC properly.
Can I find these tools in manual?
I did simulation of a system containing protein and cnt using gromacs 4.5.6.
When I see trajectory by VMD, in some
On 2/2/14, 7:15 AM, Atila Petrosian wrote:
Dear Justin and Tsjerk
you said Some tools handle PBC properly, some don't .
I want to know exactly which tools of gromacs handle PBC properly.
Can I find these tools in manual?
No, because it's not possible to test every single command that
Dear all,
I am unclear about the bond exclusion properties within gromacs. Using a
martini model system, what is the default behavior of setting
[moleculetype]
;name exclusions
eth 1
exclusions to 1? How do I find out what kind of interaction it is excluding? I
am interested in finding
On 2/2/14, 11:29 AM, Xu Dong Huang wrote:
Dear all,
I am unclear about the bond exclusion properties within gromacs. Using a
martini model system, what is the default behavior of setting
[moleculetype]
;name exclusions
eth 1
exclusions to 1? How do I find out what kind of interaction
Hi,
The first line eth1 tells it all. In that molecule all non-bonded
interactions between first bonded neighbors will be excluded.
Thus the 1-3, 1-4 (and so on) non-bonded interactions will be included. You may
add additional exclusions in the [ exclusion ] section of your topology.
Hi,
As you can see in the comment at the top of that file, you will need to
make matching changes to some arrays in src/gmxlib/names.c
Mark
On Sat, Feb 1, 2014 at 3:11 AM, Makoto Yoneya makoto-yon...@aist.go.jpwrote:
Dear Gromacs exparts:
I'd like to add the non-boded function selection
On Sun, Feb 2, 2014 at 5:29 PM, Xu Dong Huang xudonghm...@gmail.com wrote:
Dear all,
I am unclear about the bond exclusion properties within gromacs. Using a
martini model system, what is the default behavior of setting
[moleculetype]
;name exclusions
eth 1
exclusions to 1?
The
On Sun, Feb 2, 2014 at 8:28 PM, ibrahim khalil
ibrahim.khalil.c...@gmail.com wrote:
hi, i am new to gromacs. i was trying simulate multiple (eg. 3 or 4 )
carbon
nanotubes in a single box. The way I am trying to do is ...
1. Take both pdb files, merge them(using pymol) according to my
No.
Mark
On Sun, Feb 2, 2014 at 7:25 PM, Sanku M msank...@yahoo.com wrote:
Dear Gromacs users
Is it possible to simulate md of rigid spherocylinders in grimaces?
Thanks
Sanku
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Dear GMX Users,
I am trying to apply the REMD to study the difference between the folding
free energy of a 24 residue peptide with two different conformations. As I
am short of required number of processors for REMD in explicit water, I am
trying my luck with implicit solvent. I have come across
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