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

[Vito Genna]

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 the flag -s with the .tpr and then with the .gro file but in both cases I obtain a result similar to that one shown on 
PICs on link. A broken system.
Both .tpr and .gro used for the -pbc whole/nojumo/fit are ok and the system is complete.During the equillibration and for the first ~20ns of production phase
the system is stable within the box. The problem start to appear as soon as the system leaves the first box (~25ns)

Thanks in advance

V

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 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.Genna at iit.it> wrote:

> 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.
>

Sounds like you mean trjconv from your 1)a). Please be specific. If so,
IIRC, -pbc whole restores the "wholeness" as it judges from state of the -s
input. So if you made the .tpr from a .gro file that had the protein in two
chunks across periodic boundaries from the equilibration, so will the
output be split. This was what I guessed before, but you didn't report
whether you investigated whether your .tpr file contained what you think it
does. IIRC you can also use a coordinate file for -s for that stage, since
"-pbc whole" does not actually use the topology, and it is easier to
construct a .gro file that looks how you want.

Mark

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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