Dear Chris,
Thanks for your information. It is really helpful to me.
Mingjun
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Christopher Neale [chris.ne...@mail.utoronto.ca]
Sent: Friday, October 25, 2013 8:19 PM
To: gm
Dear Chris,
Thanks for your check. Yes, it should be pull_group2 for C. In this case,
the two distances have a reference group B. What about the case in which no
common reference group is shared with the two distances, e.g. distance1 is
defined as A-B and distance2 as C-D? Can current gromac
Dear GMX users,
I am going to perform the two-dimensional umbrella sampling using a pair of
distances (the distance btw atoms A and B, C and B) in the restraints. Could
someone please tell whether I can use the current pull code as follows?
-
; Pu
Dear GMX users,
I have a question about the combination of the installation parameters. I
compiled the fftw lib with --enable-sse2 and configured the gromacs with "cmake
.. -DGMX_CPU_ACCELERATION=SSE4.1". I'd like to know if it is ok to use such a
combination?
Many thanks.
Mingjun--
gmx
s.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin Lemkul [jalem...@vt.edu]
Sent: Friday, September 13, 2013 10:33 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] umbrella sampling using pull codes
On 9/12/13 10:18 PM, mjyang wrote:
> Dear Justin,
>
> Thanks for yo
.org] On Behalf
Of Justin Lemkul [jalem...@vt.edu]
Sent: Thursday, September 12, 2013 10:05 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] umbrella sampling using pull codes
On 9/12/13 9:55 AM, mjyang wrote:
> Dear GMX users,
>
> I'd like to perform the um
Dear GMX users,
I'd like to perform the umbrella sampling using the pull codes in gromacs.
The reaction coordinate is defined as the distance between the center of mass
(DCOM) of two domains in a protein. The following script is used:
--- only for pull section
; Pull code
pull
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