[gmx-users] How to efficiently fix pbc trajectories problems for VMD using

[Andrea Spitaleri]

Hi there,
have look to arrange_objects.tcl in http://people.sissa.it/~xbiarnes/tools.php. That could be useful for your task.

and

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Vito Genna
Sent: lunedì 19 maggio 2014 17:04
To: gmx-users at 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 mean that the system is stretched between two adjacent boxes showing internal bonds that run throughout the "main" pbc box (extremely long).

Regarding the steps:
Yes I already visualized the results step by step and after the 1) one trjconv fixes the bond problems but splits my protein in two distinct part (the protein contains only 1 chain) moving them in two boxes. 
At this point I use the -pbc nojump option that gives me the same previous problem (bond excessively long).

If I could reassembly the protein after -pbc whole action I'll be completely satisfied.

Any suggestion?

Thank in advance.

Cheers

Vito Genna, PhD-Fellow
Italian Institute of Technology
Drug Discovery and Development department Via Morego 30, 16163 Genoa, Italy

-------------------------------------------------------------------------------------------------------------
The process of scientific discovery is, in effect, a continual flight from wonder.
Albert Einstein


________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Mark Abraham [mark.j.abraham at 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 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 stages of 1) to see where the issue arises. If you need to, upload some pictures to a file sharing service that show what the input and unsatisfactory output was.

Mark

On Mon, May 19, 2014 at 3:15 PM, Vito Genna <Vito.Genna at iit.it> wrote:

> 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 due to its intrinsic 
> velocity in calcuating (Distances, angles, RMSD and so on) but I 
> cannot do it because I encounter a serious issue with the 
> visualization (pbc problems as you surely know) To try to avoid the 
> problem I've used several protocols, without success:
>
> 1)
>
> a) trjconv_mpi -f md_0_1.part0001.xtc -o md_0_1-whole.xtc -s 
> md_0_1.tpr -pbc whole (on the entire system)
> b) trjconv_mpi -f md_0_1-whole.xtc -o md_0_1-nojump.xtc -s md_0_1.tpr 
> -pbc nojump (on the entire system)
> c) trjconv_mpi -f md_0_1-nojump.xtc -o md_0_1-fit.xtc -s md_0_1.tpr 
> -fit progressive (on Protein only)
>
> It does not work.
>
> 2)
>
> a) trjconv_mpi -f (as the previous one) -pbc mol -ur compact -center 
> -o compact.xtc
>
> It does not work as well.
>
> 3) Option 2 changing the flag -pbc mol with -pbc res
>
> It does not work.
>
> New idea? New possible combo?
>
> Thanks in advance for your replies.
>
> All the best
>
> Vito
>
>
>
>
> Vito Genna, PhD-Fellow
> Italian Institute of Technology
> Drug Discovery and Development department Via Morego 30, 16163 Genoa, 
> Italy
>
>
> ----------------------------------------------------------------------
> ---------------------------------------
> The process of scientific discovery is, in effect, a continual flight 
> from wonder.
> Albert Einstein
>
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