enaar [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.part0
ight from
> wonder.
> Albert Einstein
>
>
>
> 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: Thursday, May 22, 2014 1
---
> The process of scientific discovery is, in effect, a continual flight from
> wonder.
> Albert Einstein
>
>
>
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [
> gromacs.org_gmx-users-
scientific discovery is, in effect, a continual flight from
> wonder.
> Albert Einstein
>
>
>
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Dallas
>
Genna
> Sent: 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
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'
from
> > wonder.
> > Albert Einstein
> >
> >
> >
> > 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]
>
nesday, 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?
> If it does (everythin
x-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?
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 t
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,
Tsjerk
On Wed, May 21, 2014 at 12:50 PM, Vito Genna wr
naar [tsje...@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 wr
t;
> -
> > The process of scientific discovery is, in effect, a continual flight
> from
> > wonder.
> > Albert Einstein
> >
> >
> > ___
l.com]
Sent: Tuesday, May 20, 2014 9:37 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for
VMD using
Hi Vito,
If the .tpr file is good, i.e. has everything assembled the way you want,
then the first step is trjconv -pbc nojump. That
st.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,
>
> Was the structure alr
-boun...@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,
s.kth.se [
> 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
>
&g
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,
You can see the results of -pbc whole and -pbc nojump on this pics
http://wikisend.com/download/777
h.se
[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:
> De
ay, May 19, 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 wrote:
Dear Mark,
Thank you for you prompt reply.
Yes, indeed I was following the suggested trjcon
ndrea
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 u
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 wrote:
> Dear Mark,
>
> Thank you for you prompt reply.
> Yes, indeed I was following the suggested trjconv workflow. Right you are.
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
un...@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 prob
romacs.org_gmx-users-boun...@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
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
Hi to everybody,
My name is Vito and I would like to share with you (and discuss also) the
problems that I have found during my TRJs analysis.
I have a system made by: Protein + dsDNA + Ligand. I obtained my single
precision trajectory in a .xtc file.
Well, I'd like to analyze my TRJs using VMD
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