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-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 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 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-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 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.ge...@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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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
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