On 10/11/10 22:28, Justin A. Lemkul wrote:
First, let me see if I understand it correctly. From your explanation
(and intuition), it seems that the issue is that "center of mass" in a
periodic environment is ambiguous -there are always (at least) two
alternate configurations that have the center
ms wrote:
On 10/11/10 21:34, Justin A. Lemkul wrote:
ms wrote:
On 09/11/10 21:36, Justin A. Lemkul wrote:
There are numerous -pbc options with trjconv; have you tried others? I
have never had luck with -pbc nojump actually working, and -pbc atom
provides no guarantee that molecules will b
On 10/11/10 21:34, Justin A. Lemkul wrote:
ms wrote:
On 09/11/10 21:36, Justin A. Lemkul wrote:
There are numerous -pbc options with trjconv; have you tried others? I
have never had luck with -pbc nojump actually working, and -pbc atom
provides no guarantee that molecules will be properly re
ms wrote:
On 09/11/10 21:36, Justin A. Lemkul wrote:
There are numerous -pbc options with trjconv; have you tried others? I
have never had luck with -pbc nojump actually working, and -pbc atom
provides no guarantee that molecules will be properly reconstructed.
Using -pbc mol -center is often
On 09/11/10 21:36, Justin A. Lemkul wrote:
There are numerous -pbc options with trjconv; have you tried others? I
have never had luck with -pbc nojump actually working, and -pbc atom
provides no guarantee that molecules will be properly reconstructed.
Using -pbc mol -center is often a much bette
On 09/11/10 21:36, Justin A. Lemkul wrote:
I am doing REMD simulations of multiple homopolymeric peptides in a
PBC box, in vacuum (it's a custom coarse grain). GROMACS 4.0.5. I want
to analyze features of the system that require to use g_gyrate to find
out the moments of inertia of the system, fo
ms wrote:
Hi,
I am doing REMD simulations of multiple homopolymeric peptides in a PBC
box, in vacuum (it's a custom coarse grain). GROMACS 4.0.5. I want to
analyze features of the system that require to use g_gyrate to find out
the moments of inertia of the system, for example.
I understa
Hi,
I am doing REMD simulations of multiple homopolymeric peptides in a PBC
box, in vacuum (it's a custom coarse grain). GROMACS 4.0.5. I want to
analyze features of the system that require to use g_gyrate to find out
the moments of inertia of the system, for example.
I understand g_gyrate i
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