...@gromacs.org] On Behalf
Of Justin Lemkul [jalem...@vt.edu]
Sent: Monday, August 12, 2013 12:55 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Implement a modified pull module to mdrun
On 8/12/13 1:29 PM, Li, Hualin wrote:
> Hi Justin,
>
> Thank you for your repl
Hi Justin,
Thank you for your reply. I also suspect that they may use like " change
pull source code -->recomplie GROMACS -->run modified mdrun ". Do you know
where the source code of the pull code is located please?
Thanks,
--H L
From: gmx-users-bo
Hi all,
I found one paper talking about they "implement a wall potential in the
pull module of the mdrun program". Does anybody know how they do it please? Is
it the similar method introduced in "User-specified potential functions" by
using following in mdp:
rilst = 1.0
coulombtype =user
Dear all,
I am simulating a system with a mix-lipid membrane, say lipid A (10%, in
the upper layer only) and lipid B (90%, in both upper and lower layer). I want
to restrain the lipid A in a certain area in the upper leaflet (It is still
moving, but can not escape from a circle). Is there
-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Mark Abraham [mark.abra...@anu.edu.au]
Sent: Monday, January 23, 2012 3:22 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] PSF file in martini force field
On 24/01/2012 4:20 AM, Li, Hualin wrote:
> Hi
Hi all,
I am running Gromacs on the system of several proteins on the membrane
using martini force field.From the output files, if I want to generate the PSF
files from them , is there any easy way to do it please?
Thanks in advance.
Regards,
Hualin--
gmx-users mailing listgmx-users
Hi all,
I am running Gromacs on the system of several proteins on the membrane
using martini force field.From the output files, if I want to generate the PSF
files from them , is there any easy way to do it please?
Thanks in advance.
Regards,
Hualin--
gmx-users mailing listgmx-users
for GROMACS users
Subject: Re: RE: [gmx-users] Martini force field: elastic network
Hi Hualin,
The elastic network should work; the help should be updated...
Note that only the 'elnedyn' method has really been tested.
Cheers,
Tsjerk
On Oct 14, 2011 7:11 PM, "Li, Hualin&
onday in
Lausanne.
The manner of the construction you describe in your email is not the
proper way to do it!
The new script is doing it properly.
If you want the old script to only generate the elastic network (as it
seems from your email) you may have it or use the scripts from the
ElNeDyn ap
Dear all,
I am using martini force field to generate elastic network for my
protein. I generate a list of distance between all beads within a certain
distance by:
genrestr -f ***.gro -n index.ndx -constr -o constraints
getting the constraints.itp file and will continue
Oh, I did installation on supercomputer before. Because you are not root user,
in the step "./configure", maybe you should use "./configure
--prefix=/home/yourname/..." to change the default installation directory.
Just my two cents. Hope it helps.
--hualin
_
Dear GMX users,
I am using pull code to make a distance restrain to my proteins and
membrane,which looks like this:
pull = umbrella
pull_geometry= cylinder
pull_vec1 = 0 0 1
pull_r1 = 2.5
pull_r0 = 2.5
pull_dim = N
Dear GMX users,
I am using pull code to make a distance restrain to my proteins and
membrane,which looks like this:
pull = umbrella
pull_geometry= cylinder
pull_vec1 = 0 0 1
pull_r1 = 2.5
pull_r0 = 2.5
pull_dim =
Dear GMX users,
I am using pull code to make a distance restrain to my proteins and
membrane,which looks like this:
pull = umbrella
pull_geometry= cylinder
pull_vec1 = 0 0 1
pull_r1 = 2.5
pull_r0 = 2.5
pull_dim =
] Center of mass: distance restrain for groups
Li, Hualin wrote:
> Hi, Justin,
>
> Thank you very much for your reply. I use the following pull code in my
> mdp file:
> "
> pull = umbrella
> pull_geometry= distance
> pull_dim
[gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, September 26, 2011 1:32 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Center of mass: distance restrain for groups
Justin A. Lemkul wrote:
>
>
> Li, Hualin wrote:
>> I a
ce restrain for groups
Li, Hualin wrote:
> Dear GMX users,
>
>How are you doing? I have a question about using distance restrain in
> GROMACS, have you ever use the distance restrain to between the protein and
> the center of mass of membrane. In gromacs, I can not find the opt
ase?
Thanks,
Hualin
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, September 26, 2011 12:05 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Center of mass: distance restrain for groups
Li, Hual
Dear GMX users,
How are you doing? I have a question about using distance restrain in
GROMACS, have you ever use the distance restrain to between the protein and the
center of mass of membrane. In gromacs, I can not find the option to choose the
center of mass of specific groups like membra
19 matches
Mail list logo
