Hi Lina,
You first remove the jumps from the trajectory. Then you can view that
trajectory with ngmx or with VMD. You can also then extract the frames
around the 'jump' and look at them. But if the molecule goes unstuck
and then crosses the boundary to get stuck to the protein again, it
would give
On Fri, Oct 28, 2011 at 5:37 PM, Tsjerk Wassenaar wrote:
> Hi Lina,
>
> My previous reply was from before I looked at the graph. Have you
> considered that the molecule might be taking a stroll and turn back,
Ha ... stroll?!
> or goes to another side of the protein? Have you looked at the
> trajec
Hi Lina,
My previous reply was from before I looked at the graph. Have you
considered that the molecule might be taking a stroll and turn back,
or goes to another side of the protein? Have you looked at the
trajectory, in particular at the trajectory with the jumps removed?
Cheers,
Tsjerk
On Fr
Hi Lina,
Don't combine fitting, centering and pbc options. It may not work as
expected. That's why the workflow is given. Use separate passes. By the way,
first centering on the protein followed by putting molecules in the box
should also work.
Cheers,
Tsjerk
On Oct 28, 2011 9:01 AM, "lina" wr
On Fri, Oct 28, 2011 at 12:34 PM, Tsjerk Wassenaar wrote:
> Hi Lina,
>
> Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump
>
> Hope it helps,
Hi,
Thanks.
I tried trjconv_g -fit translation -pbc nojump, ideally it should work.
but still not,
after I tried the minidis
Vijaya,
Can you explain how you think that may help solve the problem? I think it
won't.
Tsjerk
On Oct 28, 2011 7:40 AM, "vijaya subramanian" wrote:
-pbc atom
--
Date: Fri, 28 Oct 2011 06:34:28 +0200
Subject: Re: [gmx-users] trjconv and
-pbc atom
Date: Fri, 28 Oct 2011 06:34:28 +0200
Subject: Re: [gmx-users] trjconv and -pbc
From: tsje...@gmail.com
To: gmx-users@gromacs.org
Hi Lina,
Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump
Hope it helps,
Tsjerk
On Oct 28, 2011 6:27 AM, "lina" wrot
Hi Lina,
Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump
Hope it helps,
Tsjerk
On Oct 28, 2011 6:27 AM, "lina" wrote:
On Fri, Oct 28, 2011 at 11:48 AM, Tsjerk Wassenaar
wrote: > Hi Lina, > > Make su...
I used the initial mdrun .tpr. After checking the generated p
On Fri, Oct 28, 2011 at 11:48 AM, Tsjerk Wassenaar wrote:
> Hi Lina,
>
> Make sure to use a reference in which the molecules are together (clustered)
> the way you want them.
I used the initial mdrun .tpr. After checking the generated pdb (total
51 frames), the first 28/29 frames both are togethe
On Fri, Oct 28, 2011 at 11:47 AM, Mark Abraham wrote:
> On 28/10/2011 2:39 PM, lina wrote:
>>
>> On Thu, Oct 27, 2011 at 6:11 PM, Marzinek, Jan
>> wrote:
>>>
>>>
>>> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
>>> behalf of lina
Hi Lina,
Make sure to use a reference in which the molecules are together (clustered)
the way you want them.
Cheers,
Tsjerk
On Oct 27, 2011 11:47 AM, "lina" wrote:
Hi,
I have a problem using
trjconv_g -pbc nojump
or
trjconv_g -pbc nojump -center
I even tried the -pbc whole.
The system is
On 28/10/2011 2:39 PM, lina wrote:
On Thu, Oct 27, 2011 at 6:11 PM, Marzinek, Jan
wrote:
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of lina [lina.lastn...@gmail.com]
Sent: Thursday, October 27, 2011 10:47 AM
To: Discu
On Thu, Oct 27, 2011 at 6:11 PM, Marzinek, Jan
wrote:
>
>
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
> of lina [lina.lastn...@gmail.com]
> Sent: Thursday, October 27, 2011 10:47 AM
> To: Discussion list for GROMACS user
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of lina [lina.lastn...@gmail.com]
Sent: Thursday, October 27, 2011 10:47 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] trjconv and -pbc
Hi,
I have a problem usi
14 matches
Mail list logo
