Re: [gmx-users] very strange phenomenon for my production MD by gromacs

[Mark Abraham]

Hi,

If this "separation" was real, would you have expected to see

a) a massive spike in the potential energy
b) complete inability for the constraint algorithm to enforce bond lengths?

Hint, you haven't seen that.

Mark

On Thu, Apr 14, 2016 at 11:52 AM Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 4/14/16 5:35 AM, Brett wrote:
> > Dear All,
> >
> >
> >
> > Thanks the reply.
> >
> >
> > But I think I need to discuss with you further on whether I need to
> discontinue my production MD. As I mentioned, resi 366-367 separated from
> the major body of the protein. By pymol I find resi 366-367 were at one
> edge of the box and were almost outside of the water box, and its
> neighbouring residues resi 365 and resi 368 were at the opposite edge of
> the box and were also almost outside of the water box.
> >
> >
> > It seems that way, although at the initial step by editconf I have put
> the protein in the center of the cubic box (1.5 nm), during the first 6 ns
> the protein has moved significantly in the box, and at some moment resi
> 366-367 have moved out of the box, leading to the disconnection of resi
> 366-367 from the major body of the protein and finally leading to resi
> 366-367 at the opposite of  its neighbouring residues resi 365 and resi 368
> in the cubix box.
> >
> >
> > Am I right?
> >
>
> Diffusion is normal.  The residues are not actually disconnected.  You can
> use
> trjconv to "fix" this state, but there is nothing physically wrong with it.
> mdrun cares about physics, not our visualization convenience.
>
> -Justin
>
> >
> > Brett
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > At 2016-04-14 16:31:20, "Mark Abraham" <mark.j.abra...@gmail.com> wrote:
> >> Hi,
> >>
> >> As the link Justin gave you says, and Tsjerk has since confirmed, this
> is
> >> normal. There are infinitely many equivalent representations of your
> >> simulation, not all of which will look connected for the thing that is
> of
> >> interest.
> >>
> >> Strategies for handling visualisation are also on that link, but you
> don't
> >> need to handle anything within the simulation.
> >>
> >> Mark
> >>
> >> On Thu, 14 Apr 2016 09:48 Brett <brettliu...@163.com> wrote:
> >>
> >>> Dear All,
> >>>
> >>> As I have introduced in my previous e-mail,
> >>>
> >>> "After energy minimization and equilibrations, I am now running a 50 ns
> >>> production MD, for a protein of 6 identical subunits, with each subunit
> >>> about 300 residues (from resi 120 to resi 420), and there were no
> breaks in
> >>> any chain. Every day it runs about 1 ns, and every day I use the
> command
> >>> trjconv to get a new PDB based on the md_0_1.trr file, for the
> comparison
> >>> between the new pdb and the initial pdb.
> >>>
> >>>
> >>> Today I got the PDB at 6 ns. However when I checked it my pymol, I find
> >>> there is something very strange. Although the rmsd between the 6 ns md
> PDB
> >>> and 0ns md PDB was about only 3.7, for chain B, residue 366-367 moved
> 180
> >>> angstrom away from this residues neighbouring residues, and
> correspondingly
> >>> make chain B has a break at residue 366-367!"
> >>>
> >>> A moment ago by trjconv I regot the6 ns pdb with water, I find the
> residue
> >>> 366-367 are almost (or exactly) at the edge of the water box (but by
> naked
> >>> eye it seems the residue 366-367 are not outside of the water box). In
> this
> >>> does the moving away of the residue 366-367 are still caused by "
> >>> Periodic_Boundary_Conditions", and can I continue the production md to
> >>> completion with the residue 366-367 disconnected from the major part
> of the
> >>> protein complex and then I correct it by trjconv?
> >>>
> >>> I am looking forward to getting a reply from you.
> >>>
> >>>
> >>> Brett
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>  Forwarding messages 
> >>> From: "Tsjerk Wassenaar" <tsje...@gmail.com>
> >>> Date: 2016-04-14 12:16:56
> >>> To:  "Discussion list for GROMACS users" &

Re: [gmx-users] very strange phenomenon for my production MD by gromacs

[Justin Lemkul]

On 4/14/16 5:35 AM, Brett wrote:

Dear All,



Thanks the reply.


But I think I need to discuss with you further on whether I need to discontinue 
my production MD. As I mentioned, resi 366-367 separated from the major body of 
the protein. By pymol I find resi 366-367 were at one edge of the box and were 
almost outside of the water box, and its neighbouring residues resi 365 and 
resi 368 were at the opposite edge of the box and were also almost outside of 
the water box.


It seems that way, although at the initial step by editconf I have put the 
protein in the center of the cubic box (1.5 nm), during the first 6 ns the 
protein has moved significantly in the box, and at some moment resi 366-367 
have moved out of the box, leading to the disconnection of resi 366-367 from 
the major body of the protein and finally leading to resi 366-367 at the 
opposite of  its neighbouring residues resi 365 and resi 368 in the cubix box.


Am I right?



Diffusion is normal.  The residues are not actually disconnected.  You can use 
trjconv to "fix" this state, but there is nothing physically wrong with it. 
mdrun cares about physics, not our visualization convenience.


-Justin



Brett









At 2016-04-14 16:31:20, "Mark Abraham" <mark.j.abra...@gmail.com> wrote:

Hi,

As the link Justin gave you says, and Tsjerk has since confirmed, this is
normal. There are infinitely many equivalent representations of your
simulation, not all of which will look connected for the thing that is of
interest.

Strategies for handling visualisation are also on that link, but you don't
need to handle anything within the simulation.

Mark

On Thu, 14 Apr 2016 09:48 Brett <brettliu...@163.com> wrote:


Dear All,

As I have introduced in my previous e-mail,

"After energy minimization and equilibrations, I am now running a 50 ns
production MD, for a protein of 6 identical subunits, with each subunit
about 300 residues (from resi 120 to resi 420), and there were no breaks in
any chain. Every day it runs about 1 ns, and every day I use the command
trjconv to get a new PDB based on the md_0_1.trr file, for the comparison
between the new pdb and the initial pdb.


Today I got the PDB at 6 ns. However when I checked it my pymol, I find
there is something very strange. Although the rmsd between the 6 ns md PDB
and 0ns md PDB was about only 3.7, for chain B, residue 366-367 moved 180
angstrom away from this residues neighbouring residues, and correspondingly
make chain B has a break at residue 366-367!"

A moment ago by trjconv I regot the6 ns pdb with water, I find the residue
366-367 are almost (or exactly) at the edge of the water box (but by naked
eye it seems the residue 366-367 are not outside of the water box). In this
does the moving away of the residue 366-367 are still caused by "
Periodic_Boundary_Conditions", and can I continue the production md to
completion with the residue 366-367 disconnected from the major part of the
protein complex and then I correct it by trjconv?

I am looking forward to getting a reply from you.


Brett










 Forwarding messages 
From: "Tsjerk Wassenaar" <tsje...@gmail.com>
Date: 2016-04-14 12:16:56
To:  "Discussion list for GROMACS users" <gmx-us...@gromacs.org>
Subject: Re: [gmx-users] very strange phenomenon for my production MD by
gromacs
right!

Cheers,

Tsjerk
On Apr 14, 2016 05:32, "Brett" <brettliu...@163.com> wrote:


Dear All,

If the issue in my production MD was caused by
"Periodic_Boundary_Conditions", I can continue my production MD until it
completed, and it will not affect my final results suppose I have it
corrected by trjconv, right?


Brett











At 2016-04-13 22:37:34, "Justin Lemkul" <jalem...@vt.edu> wrote:



On 4/13/16 10:30 AM, Brett wrote:

Dear All,


After energy minimization and equilibrations, I am now running a 50 ns
production MD, for a protein of 6 identical subunits, with each

subunit

about

300 residues (from resi 120 to resi 420), and there were no breaks in

any

chain. Every day it runs about 1 ns, and every day I use the command

trjconv

to get a new PDB based on the md_0_1.trr file, for the comparison

between the

new pdb and the initial pdb.


Today I got the PDB at 6 ns. However when I checked it my pymol, I

find

there

is something very strange. Although the rmsd between the 6 ns md PDB

and 0ns

md PDB was about only 3.7, for chain B, residue 366-367 moved 180

angstrom

away from this residues neighbouring residues, and correspondingly

make

chain

B has a break at residue 366-367!


Will you please let me know what is wrong with my MD, and why 2

residues

(resi 366-367) moved 180 angstrom away? Does this phenomenon often

occur?








http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions


-Justin

--
==

Justin A. Lemkul

[gmx-users] very strange phenomenon for my production MD by gromacs

[Brett]

Dear All,



Thanks the reply.


But I think I need to discuss with you further on whether I need to discontinue 
my production MD. As I mentioned, resi 366-367 separated from the major body of 
the protein. By pymol I find resi 366-367 were at one edge of the box and were 
almost outside of the water box, and its neighbouring residues resi 365 and 
resi 368 were at the opposite edge of the box and were also almost outside of 
the water box.


It seems that way, although at the initial step by editconf I have put the 
protein in the center of the cubic box (1.5 nm), during the first 6 ns the 
protein has moved significantly in the box, and at some moment resi 366-367 
have moved out of the box, leading to the disconnection of resi 366-367 from 
the major body of the protein and finally leading to resi 366-367 at the 
opposite of  its neighbouring residues resi 365 and resi 368 in the cubix box.


Am I right?


Brett









At 2016-04-14 16:31:20, "Mark Abraham" <mark.j.abra...@gmail.com> wrote:
>Hi,
>
>As the link Justin gave you says, and Tsjerk has since confirmed, this is
>normal. There are infinitely many equivalent representations of your
>simulation, not all of which will look connected for the thing that is of
>interest.
>
>Strategies for handling visualisation are also on that link, but you don't
>need to handle anything within the simulation.
>
>Mark
>
>On Thu, 14 Apr 2016 09:48 Brett <brettliu...@163.com> wrote:
>
>> Dear All,
>>
>> As I have introduced in my previous e-mail,
>>
>> "After energy minimization and equilibrations, I am now running a 50 ns
>> production MD, for a protein of 6 identical subunits, with each subunit
>> about 300 residues (from resi 120 to resi 420), and there were no breaks in
>> any chain. Every day it runs about 1 ns, and every day I use the command
>> trjconv to get a new PDB based on the md_0_1.trr file, for the comparison
>> between the new pdb and the initial pdb.
>>
>>
>> Today I got the PDB at 6 ns. However when I checked it my pymol, I find
>> there is something very strange. Although the rmsd between the 6 ns md PDB
>> and 0ns md PDB was about only 3.7, for chain B, residue 366-367 moved 180
>> angstrom away from this residues neighbouring residues, and correspondingly
>> make chain B has a break at residue 366-367!"
>>
>> A moment ago by trjconv I regot the6 ns pdb with water, I find the residue
>> 366-367 are almost (or exactly) at the edge of the water box (but by naked
>> eye it seems the residue 366-367 are not outside of the water box). In this
>> does the moving away of the residue 366-367 are still caused by "
>> Periodic_Boundary_Conditions", and can I continue the production md to
>> completion with the residue 366-367 disconnected from the major part of the
>> protein complex and then I correct it by trjconv?
>>
>> I am looking forward to getting a reply from you.
>>
>>
>> Brett
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>  Forwarding messages 
>> From: "Tsjerk Wassenaar" <tsje...@gmail.com>
>> Date: 2016-04-14 12:16:56
>> To:  "Discussion list for GROMACS users" <gmx-us...@gromacs.org>
>> Subject: Re: [gmx-users] very strange phenomenon for my production MD by
>> gromacs
>> right!
>>
>> Cheers,
>>
>> Tsjerk
>> On Apr 14, 2016 05:32, "Brett" <brettliu...@163.com> wrote:
>>
>> > Dear All,
>> >
>> > If the issue in my production MD was caused by
>> > "Periodic_Boundary_Conditions", I can continue my production MD until it
>> > completed, and it will not affect my final results suppose I have it
>> > corrected by trjconv, right?
>> >
>> >
>> > Brett
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > At 2016-04-13 22:37:34, "Justin Lemkul" <jalem...@vt.edu> wrote:
>> > >
>> > >
>> > >On 4/13/16 10:30 AM, Brett wrote:
>> > >> Dear All,
>> > >>
>> > >>
>> > >> After energy minimization and equilibrations, I am now running a 50 ns
>> > >> production MD, for a protein of 6 identical subunits, with each
>> subunit
>> > about
>> > >> 300 residues (from resi 120 to resi 420), and there were no breaks in
>> > any
>> > >> chain. Every day it runs about 1 ns, and every day I use the command
>> > trjconv
>>

Re: [gmx-users] very strange phenomenon for my production MD by gromacs

[Mark Abraham]

Hi,

As the link Justin gave you says, and Tsjerk has since confirmed, this is
normal. There are infinitely many equivalent representations of your
simulation, not all of which will look connected for the thing that is of
interest.

Strategies for handling visualisation are also on that link, but you don't
need to handle anything within the simulation.

Mark

On Thu, 14 Apr 2016 09:48 Brett <brettliu...@163.com> wrote:

> Dear All,
>
> As I have introduced in my previous e-mail,
>
> "After energy minimization and equilibrations, I am now running a 50 ns
> production MD, for a protein of 6 identical subunits, with each subunit
> about 300 residues (from resi 120 to resi 420), and there were no breaks in
> any chain. Every day it runs about 1 ns, and every day I use the command
> trjconv to get a new PDB based on the md_0_1.trr file, for the comparison
> between the new pdb and the initial pdb.
>
>
> Today I got the PDB at 6 ns. However when I checked it my pymol, I find
> there is something very strange. Although the rmsd between the 6 ns md PDB
> and 0ns md PDB was about only 3.7, for chain B, residue 366-367 moved 180
> angstrom away from this residues neighbouring residues, and correspondingly
> make chain B has a break at residue 366-367!"
>
> A moment ago by trjconv I regot the6 ns pdb with water, I find the residue
> 366-367 are almost (or exactly) at the edge of the water box (but by naked
> eye it seems the residue 366-367 are not outside of the water box). In this
> does the moving away of the residue 366-367 are still caused by "
> Periodic_Boundary_Conditions", and can I continue the production md to
> completion with the residue 366-367 disconnected from the major part of the
> protein complex and then I correct it by trjconv?
>
> I am looking forward to getting a reply from you.
>
>
> Brett
>
>
>
>
>
>
>
>
>
>
>  Forwarding messages 
> From: "Tsjerk Wassenaar" <tsje...@gmail.com>
> Date: 2016-04-14 12:16:56
> To:  "Discussion list for GROMACS users" <gmx-us...@gromacs.org>
> Subject: Re: [gmx-users] very strange phenomenon for my production MD by
> gromacs
> right!
>
> Cheers,
>
> Tsjerk
> On Apr 14, 2016 05:32, "Brett" <brettliu...@163.com> wrote:
>
> > Dear All,
> >
> > If the issue in my production MD was caused by
> > "Periodic_Boundary_Conditions", I can continue my production MD until it
> > completed, and it will not affect my final results suppose I have it
> > corrected by trjconv, right?
> >
> >
> > Brett
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > At 2016-04-13 22:37:34, "Justin Lemkul" <jalem...@vt.edu> wrote:
> > >
> > >
> > >On 4/13/16 10:30 AM, Brett wrote:
> > >> Dear All,
> > >>
> > >>
> > >> After energy minimization and equilibrations, I am now running a 50 ns
> > >> production MD, for a protein of 6 identical subunits, with each
> subunit
> > about
> > >> 300 residues (from resi 120 to resi 420), and there were no breaks in
> > any
> > >> chain. Every day it runs about 1 ns, and every day I use the command
> > trjconv
> > >> to get a new PDB based on the md_0_1.trr file, for the comparison
> > between the
> > >> new pdb and the initial pdb.
> > >>
> > >>
> > >> Today I got the PDB at 6 ns. However when I checked it my pymol, I
> find
> > there
> > >> is something very strange. Although the rmsd between the 6 ns md PDB
> > and 0ns
> > >> md PDB was about only 3.7, for chain B, residue 366-367 moved 180
> > angstrom
> > >> away from this residues neighbouring residues, and correspondingly
> make
> > chain
> > >> B has a break at residue 366-367!
> > >>
> > >>
> > >> Will you please let me know what is wrong with my MD, and why 2
> residues
> > >> (resi 366-367) moved 180 angstrom away? Does this phenomenon often
> > occur?
> > >>
> > >
> > >
> >
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> > >
> > >-Justin
> > >
> > >--
> > >==
> > >
> > >Justin A. Lemkul, Ph.D.
> > >Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > >Department of Pharmaceutical Sciences
> > >School of Pharmacy
> > >Health Sciences Facility II,

[gmx-users] very strange phenomenon for my production MD by gromacs

[Brett]

Dear All,

As I have introduced in my previous e-mail,

"After energy minimization and equilibrations, I am now running a 50 ns 
production MD, for a protein of 6 identical subunits, with each subunit about 
300 residues (from resi 120 to resi 420), and there were no breaks in any 
chain. Every day it runs about 1 ns, and every day I use the command trjconv to 
get a new PDB based on the md_0_1.trr file, for the comparison between the new 
pdb and the initial pdb.


Today I got the PDB at 6 ns. However when I checked it my pymol, I find there 
is something very strange. Although the rmsd between the 6 ns md PDB and 0ns md 
PDB was about only 3.7, for chain B, residue 366-367 moved 180 angstrom away 
from this residues neighbouring residues, and correspondingly make chain B has 
a break at residue 366-367!"

A moment ago by trjconv I regot the6 ns pdb with water, I find the residue 
366-367 are almost (or exactly) at the edge of the water box (but by naked eye 
it seems the residue 366-367 are not outside of the water box). In this does 
the moving away of the residue 366-367 are still caused by "
Periodic_Boundary_Conditions", and can I continue the production md to 
completion with the residue 366-367 disconnected from the major part of the 
protein complex and then I correct it by trjconv?

I am looking forward to getting a reply from you.


Brett










 Forwarding messages 
From: "Tsjerk Wassenaar" <tsje...@gmail.com>
Date: 2016-04-14 12:16:56
To:  "Discussion list for GROMACS users" <gmx-us...@gromacs.org>
Subject: Re: [gmx-users] very strange phenomenon for my production MD by gromacs
right!

Cheers,

Tsjerk
On Apr 14, 2016 05:32, "Brett" <brettliu...@163.com> wrote:

> Dear All,
>
> If the issue in my production MD was caused by
> "Periodic_Boundary_Conditions", I can continue my production MD until it
> completed, and it will not affect my final results suppose I have it
> corrected by trjconv, right?
>
>
> Brett
>
>
>
>
>
>
>
>
>
>
>
> At 2016-04-13 22:37:34, "Justin Lemkul" <jalem...@vt.edu> wrote:
> >
> >
> >On 4/13/16 10:30 AM, Brett wrote:
> >> Dear All,
> >>
> >>
> >> After energy minimization and equilibrations, I am now running a 50 ns
> >> production MD, for a protein of 6 identical subunits, with each subunit
> about
> >> 300 residues (from resi 120 to resi 420), and there were no breaks in
> any
> >> chain. Every day it runs about 1 ns, and every day I use the command
> trjconv
> >> to get a new PDB based on the md_0_1.trr file, for the comparison
> between the
> >> new pdb and the initial pdb.
> >>
> >>
> >> Today I got the PDB at 6 ns. However when I checked it my pymol, I find
> there
> >> is something very strange. Although the rmsd between the 6 ns md PDB
> and 0ns
> >> md PDB was about only 3.7, for chain B, residue 366-367 moved 180
> angstrom
> >> away from this residues neighbouring residues, and correspondingly make
> chain
> >> B has a break at residue 366-367!
> >>
> >>
> >> Will you please let me know what is wrong with my MD, and why 2 residues
> >> (resi 366-367) moved 180 angstrom away? Does this phenomenon often
> occur?
> >>
> >
> >
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> >
> >-Justin
> >
> >--
> >==
> >
> >Justin A. Lemkul, Ph.D.
> >Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> >Department of Pharmaceutical Sciences
> >School of Pharmacy
> >Health Sciences Facility II, Room 629
> >University of Maryland, Baltimore
> >20 Penn St.
> >Baltimore, MD 21201
> >
> >jalem...@outerbanks.umaryland.edu | (410) 706-7441
> >http://mackerell.umaryland.edu/~jalemkul
> >
> >==
> >--
> >Gromacs Users mailing list
> >
> >* Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> >* For (un)subscribe requests visit
> >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> http

Re: [gmx-users] very strange phenomenon for my production MD by gromacs

[Tsjerk Wassenaar]

right!

Cheers,

Tsjerk
On Apr 14, 2016 05:32, "Brett"  wrote:

> Dear All,
>
> If the issue in my production MD was caused by
> "Periodic_Boundary_Conditions", I can continue my production MD until it
> completed, and it will not affect my final results suppose I have it
> corrected by trjconv, right?
>
>
> Brett
>
>
>
>
>
>
>
>
>
>
>
> At 2016-04-13 22:37:34, "Justin Lemkul"  wrote:
> >
> >
> >On 4/13/16 10:30 AM, Brett wrote:
> >> Dear All,
> >>
> >>
> >> After energy minimization and equilibrations, I am now running a 50 ns
> >> production MD, for a protein of 6 identical subunits, with each subunit
> about
> >> 300 residues (from resi 120 to resi 420), and there were no breaks in
> any
> >> chain. Every day it runs about 1 ns, and every day I use the command
> trjconv
> >> to get a new PDB based on the md_0_1.trr file, for the comparison
> between the
> >> new pdb and the initial pdb.
> >>
> >>
> >> Today I got the PDB at 6 ns. However when I checked it my pymol, I find
> there
> >> is something very strange. Although the rmsd between the 6 ns md PDB
> and 0ns
> >> md PDB was about only 3.7, for chain B, residue 366-367 moved 180
> angstrom
> >> away from this residues neighbouring residues, and correspondingly make
> chain
> >> B has a break at residue 366-367!
> >>
> >>
> >> Will you please let me know what is wrong with my MD, and why 2 residues
> >> (resi 366-367) moved 180 angstrom away? Does this phenomenon often
> occur?
> >>
> >
> >
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> >
> >-Justin
> >
> >--
> >==
> >
> >Justin A. Lemkul, Ph.D.
> >Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> >Department of Pharmaceutical Sciences
> >School of Pharmacy
> >Health Sciences Facility II, Room 629
> >University of Maryland, Baltimore
> >20 Penn St.
> >Baltimore, MD 21201
> >
> >jalem...@outerbanks.umaryland.edu | (410) 706-7441
> >http://mackerell.umaryland.edu/~jalemkul
> >
> >==
> >--
> >Gromacs Users mailing list
> >
> >* Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> >* For (un)subscribe requests visit
> >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
> --
> Gromacs Users mailing list
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Re: [gmx-users] very strange phenomenon for my production MD by gromacs

[Brett]

Dear All,

If the issue in my production MD was caused by "Periodic_Boundary_Conditions", 
I can continue my production MD until it completed, and it will not affect my 
final results suppose I have it corrected by trjconv, right?


Brett 











At 2016-04-13 22:37:34, "Justin Lemkul"  wrote:
>
>
>On 4/13/16 10:30 AM, Brett wrote:
>> Dear All,
>>
>>
>> After energy minimization and equilibrations, I am now running a 50 ns
>> production MD, for a protein of 6 identical subunits, with each subunit about
>> 300 residues (from resi 120 to resi 420), and there were no breaks in any
>> chain. Every day it runs about 1 ns, and every day I use the command trjconv
>> to get a new PDB based on the md_0_1.trr file, for the comparison between the
>> new pdb and the initial pdb.
>>
>>
>> Today I got the PDB at 6 ns. However when I checked it my pymol, I find there
>> is something very strange. Although the rmsd between the 6 ns md PDB and 0ns
>> md PDB was about only 3.7, for chain B, residue 366-367 moved 180 angstrom
>> away from this residues neighbouring residues, and correspondingly make chain
>> B has a break at residue 366-367!
>>
>>
>> Will you please let me know what is wrong with my MD, and why 2 residues
>> (resi 366-367) moved 180 angstrom away? Does this phenomenon often occur?
>>
>
>http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>
>-Justin
>
>-- 
>==
>
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>
>jalem...@outerbanks.umaryland.edu | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
>==
>-- 
>Gromacs Users mailing list
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Re: [gmx-users] very strange phenomenon for my production MD by gromacs

[Justin Lemkul]

On 4/13/16 10:30 AM, Brett wrote:

Dear All,


After energy minimization and equilibrations, I am now running a 50 ns
production MD, for a protein of 6 identical subunits, with each subunit about
300 residues (from resi 120 to resi 420), and there were no breaks in any
chain. Every day it runs about 1 ns, and every day I use the command trjconv
to get a new PDB based on the md_0_1.trr file, for the comparison between the
new pdb and the initial pdb.


Today I got the PDB at 6 ns. However when I checked it my pymol, I find there
is something very strange. Although the rmsd between the 6 ns md PDB and 0ns
md PDB was about only 3.7, for chain B, residue 366-367 moved 180 angstrom
away from this residues neighbouring residues, and correspondingly make chain
B has a break at residue 366-367!


Will you please let me know what is wrong with my MD, and why 2 residues
(resi 366-367) moved 180 angstrom away? Does this phenomenon often occur?



http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] very strange phenomenon for my production MD by gromacs

[Dries Van Rompaey]

Hi,
Sounds like you're experiencing periodic boundary artifacts. Take a look at
the following link:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Dries
On 13 Apr 2016 4:31 p.m., "Brett"  wrote:

> Dear All,
>
>
> After energy minimization and equilibrations, I am now running a 50 ns
> production MD, for a protein of 6 identical subunits, with each subunit
> about 300 residues (from resi 120 to resi 420), and there were no breaks in
> any chain. Every day it runs about 1 ns, and every day I use the command
> trjconv to get a new PDB based on the md_0_1.trr file, for the comparison
> between the new pdb and the initial pdb.
>
>
> Today I got the PDB at 6 ns. However when I checked it my pymol, I find
> there is something very strange. Although the rmsd between the 6 ns md PDB
> and 0ns md PDB was about only 3.7, for chain B, residue 366-367 moved 180
> angstrom away from this residues neighbouring residues, and correspondingly
> make chain B has a break at residue 366-367!
>
>
> Will you please let me know what is wrong with my MD, and why 2 residues
> (resi 366-367) moved 180 angstrom away? Does this phenomenon often occur?
>
>
> I am looking forward to getting a reply from you.
>
>
> Brett
> --
> Gromacs Users mailing list
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[gmx-users] very strange phenomenon for my production MD by gromacs

[Brett]

Dear All,


After energy minimization and equilibrations, I am now running a 50 ns 
production MD, for a protein of 6 identical subunits, with each subunit about 
300 residues (from resi 120 to resi 420), and there were no breaks in any 
chain. Every day it runs about 1 ns, and every day I use the command trjconv to 
get a new PDB based on the md_0_1.trr file, for the comparison between the new 
pdb and the initial pdb.


Today I got the PDB at 6 ns. However when I checked it my pymol, I find there 
is something very strange. Although the rmsd between the 6 ns md PDB and 0ns md 
PDB was about only 3.7, for chain B, residue 366-367 moved 180 angstrom away 
from this residues neighbouring residues, and correspondingly make chain B has 
a break at residue 366-367!


Will you please let me know what is wrong with my MD, and why 2 residues (resi 
366-367) moved 180 angstrom away? Does this phenomenon often occur?


I am looking forward to getting a reply from you.


Brett
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