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

Tue May 20 19:30:10 CEST 2014

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 from the first frame of your run. After you
unbroke the first frame, you can use that as reference for processing your
trajectory with -pbc nojump.

Hope it helps,

Tsjerk

On Tue, May 20, 2014 at 7:14 PM, Vito Genna <Vito.Genna at iit.it> wrote:

> Dear Justin,
>
> Thank you for your email.
> As in your case, my system is formed by a Protein + dsDNA + structural
> ions + counterions + ligand + water
> I guess that I have too much element to efficiently solve the problem but
> I want to try to fix it. The solution could help
> other people to avoid to became crazy with this kind of TRJs manipulations.
>
> Figs. link: http://wikisend.com/download/571570/pics.zip
>
> Well. today I tried  a different combo as:
>
>  A) trjconv -s -f -pbc mol(res) -center (-n index with
> DNA&Protein/Ligand/Protein)
>
> to obtain trajectories as shown in pic1
>
> B) Then i used -pbc whole/nojump to obtain a result as shown in fig 2
>
> I guess that the problem still persists....
>
> Any suggestion about your experience?
>
> 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 Justin
> Lemkul [jalemkul at vt.edu]
> Sent: Monday, May 19, 2014 11:26 PM
> To: gmx-users at 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 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)
> >
>
> Can you post an image looking straight-on at the system, with box vectors
> rendered, with and without water?  The oblique shots you've provided are a
> bit
> hard to interpret.
>
> I've dealt with very complex systems like these (multiple proteins + dsDNA
> +
> ions + ligands) and it is a pain.  I believe I went through 6 rounds of
> trjconv
> for most of them (hundreds of ns in length).  The exact protocol is highly
> system-specific, but the key is that it is often necessary to use custom
> index
> groups (a specific residue, or a few in some key location) for centering
> and/or
> fitting.
>
> -Justin
>
> > 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
> >>>
> >>> --
> >>> Gromacs Users mailing list
> >>>
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
Tsjerk A. Wassenaar, Ph.D.