: Wednesday, 21 May 2014 11:07 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] How to efficiently fix pbc trajectories
problems for VMD using
Dear Tsjerk,
No, it doesn't. (http://wikisend.com/download/324888/Post-nojump.png)
I think that the first step need to be changed that's why I tried (whit
Warren [dallas.war...@monash.edu]
Sent: Thursday, May 22, 2014 1:40 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems
for VMD using
Would suggest that each time you try a different workflow, do so in a new
subdirectory and copy the required
-boun...@maillist.sys.kth.se] on behalf of Dallas
Warren [dallas.war...@monash.edu]
Sent: Thursday, May 22, 2014 1:40 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems
for VMD using
Would suggest that each time you try a different workflow, do
...@maillist.sys.kth.se] on behalf of Tsjerk
Wassenaar [tsje...@gmail.com]
Sent: Thursday, May 22, 2014 11:10 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems
for VMD using
Hi Vito,
Does npt.tpr correspond to the first frame
[tsje...@gmail.com]
Sent: Thursday, May 22, 2014 4:06 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for
VMD using
Hey Vito,
Don't use -skip. And add -pbc nojump to that first run of trjconv:
trjconv_mpi -f md_0_1.part0001.xtc -o
...@gmail.com]
Sent: Tuesday, May 20, 2014 7:30 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems
for VMD using
Hi Vito,
Was the structure already broken up when you solvated it? If not, which
seems likely to me, then you
...@gmail.com]
Sent: Wednesday, May 21, 2014 11:58 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for
VMD using
Hey Vito,
Can you paste your exact workflow?
Cheers,
Tsjerk
On Wed, May 21, 2014 at 9:53 AM, Vito Genna vito.ge
to efficiently fix pbc trajectories problems for
VMD using
Hey Vito,
After the first step, does the trajectory (say the last frame) look fine?
If it does (everything nicely assembled), then after the second step, does
it still look fine, and is it placed properly in the center of the box?
Cheers
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [
gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tsjerk
Wassenaar [tsje...@gmail.com]
Sent: Wednesday, May 21, 2014 1:48 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] How to efficiently fix pbc
Wassenaar [tsje...@gmail.com]
Sent: Wednesday, May 21, 2014 1:48 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems
for VMD using
Hey Vito,
After the first step, does the trajectory (say the last frame) look fine
...@gromacs.org
Subject: Re: [gmx-users] How to efficiently fix pbc trajectories
problems for VMD using
Dear Tsjerk,
No, it doesn't. (http://wikisend.com/download/324888/Post-nojump.png)
I think that the first step need to be changed that's why I tried (whit
no success)
the flag -pbc whole. I'm
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul
[jalem...@vt.edu]
Sent: Monday, May 19, 2014 11:26 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for
VMD using
On 5/19/14, 12:29 PM, Vito Genna wrote:
Dear Mark
...@gromacs.org
Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems
for VMD using
On 5/19/14, 12:29 PM, Vito Genna wrote:
Dear Mark,
You can see the results of -pbc whole and -pbc nojump on this pics
http://wikisend.com/download/777550/PICs.zip
I tried to use
...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tsjerk
Wassenaar [tsje...@gmail.com]
Sent: Tuesday, May 20, 2014 7:30 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for
VMD using
Hi Vito
for GROMACS users
Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems
for VMD using
Hi Vito,
Was the structure already broken up when you solvated it? If not, which
seems likely to me, then you can use that structure, or the .tpr from the
EM in solvent, to remove jumps
You seem to be following
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions,
which is good. But it's hard to help when we don't know what you think
doesn't work means. Make sure that the things you think are whole in
md_0_1.tpr actually are. Visualize your intermediate
...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mark Abraham
[mark.j.abra...@gmail.com]
Sent: Monday, May 19, 2014 4:31 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for
VMD using
You seem
for GROMACS users
Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems
for VMD using
You seem to be following
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
,
which is good. But it's hard to help when we don't know what you think
doesn't
Genna
Sent: lunedì 19 maggio 2014 17:04
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for
VMD using
Dear Mark,
Thank you for you prompt reply.
Yes, indeed I was following the suggested trjconv workflow. Right you are. When
I say does not work I
for GROMACS users
Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for
VMD using
On Mon, May 19, 2014 at 5:03 PM, Vito Genna vito.ge...@iit.it wrote:
Dear Mark,
Thank you for you prompt reply.
Yes, indeed I was following the suggested trjconv workflow. Right you
Spitaleri [andrea.spital...@iit.it]
Sent: Monday, May 19, 2014 5:43 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for
VMD using
Hi there,
have look to arrange_objects.tcl in http://people.sissa.it/~xbiarnes/tools.php.
That could be useful
, 2014 5:32 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for
VMD using
On Mon, May 19, 2014 at 5:03 PM, Vito Genna vito.ge...@iit.it wrote:
Dear Mark,
Thank you for you prompt reply.
Yes, indeed I was following the suggested
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