OK, so there are a lot of necessary dependencies in the command...
Thank you.
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On 12/18/12 2:04 PM, zugunder wrote:
Justin Lemkul wrote
If you don't specify an actual file name to -s, then all Gromacs tools
look for a default file name, which in this case is "topol.tpr." Since
you've run a simulation, clearly you have a .tpr file, which is what you
need to provide to -s
Justin Lemkul wrote
> If you don't specify an actual file name to -s, then all Gromacs tools
> look for a default file name, which in this case is "topol.tpr." Since
> you've run a simulation, clearly you have a .tpr file, which is what you
> need to provide to -s.
I have only one .tpr file - the
On 12/18/12 1:44 PM, zugunder wrote:
Justin Lemkul wrote
You need a .tpr file and can re-wrap the periodic image with trjconv -pbc
mol -ur compact.
Funny, it needs a file which I don't find:
g_trjconv -f nvt_minimized.trr -o nvt_minimized_compact.xtc -pbc mol -ur
compact
Program g_trjconv,
Justin Lemkul wrote
> You need a .tpr file and can re-wrap the periodic image with trjconv -pbc
> mol -ur compact.
Funny, it needs a file which I don't find:
g_trjconv -f nvt_minimized.trr -o nvt_minimized_compact.xtc -pbc mol -ur
compact
Program g_trjconv, VERSION 4.5.5
Source code file: /build
On 12/17/12 3:04 PM, zugunder wrote:
Justin Lemkul wrote
It is calculated correctly, the math is just a bit more complex (see the
manual for the equations). The distance to the box edge is defined the
same way, but the two approaches don't necessarily give equally suitable
results. Consider
Justin Lemkul wrote
> It is calculated correctly, the math is just a bit more complex (see the
> manual for the equations). The distance to the box edge is defined the
> same way, but the two approaches don't necessarily give equally suitable
> results. Consider the first case, which produces a r
On 12/17/12 2:14 PM, zugunder wrote:
Thank you, Justin, for the prompt answer!
Justin Lemkul wrote
In almost all cases, a dodecahedral box is the optimal choice. A cubic
box with the same periodic distance for an elongated protein would be much
larger.
OK, got it.
Justin Lemkul wrote
I
Thank you, Justin, for the prompt answer!
Justin Lemkul wrote
> In almost all cases, a dodecahedral box is the optimal choice. A cubic
> box with the same periodic distance for an elongated protein would be much
> larger.
OK, got it.
Justin Lemkul wrote
> In the absence of the actual editcon
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