Re: [gmx-users] PBC after energy minimization

[Justin Lemkul]

On 5/1/20 9:29 AM, John Whittaker wrote:

Hi Mohamed,


Hello everybody,

In order to solve the PBC at the end I use the command:

*gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_noPBC.xtc -pbc mol *

followed by:

*gmx trjconv -s md_0_1.tpr  -f md_noPBC.xtc -o md_noPBC.pdb*


I want to solve this problem after the energy minimization but I don't
have
.xtc file to use it as I do at the end.

How can I solve this problem after the energy minimization ?

You're saying that your energy minimization does not produce a trajectory
(a .trr or .xtc file)?

If that's the case, you just have to instruct GROMACS to periodically
write to a trajectory file using options in the .mdp file (namely,
nstxout). Take a look at:

http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html

Under the section "output control" you will find what you are looking for.


"Trajectories" from energy minimization are generally unreadable as the 
interval of saved frames is uneven. During EM, a frame is only written 
when the energy goes down, which is not necessarily every possible 
frame. I also seem to recall that there is never XTC output from EM, 
even if requested, because it's rather pointless. Maybe that has changed.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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.

Re: [gmx-users] PBC after energy minimization

[John Whittaker]

Hi Mohamed,

> Hello everybody,
>
> In order to solve the PBC at the end I use the command:
>
> *gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_noPBC.xtc -pbc mol *
>
> followed by:
>
> *gmx trjconv -s md_0_1.tpr  -f md_noPBC.xtc -o md_noPBC.pdb*
>
>
> I want to solve this problem after the energy minimization but I don't
> have
> .xtc file to use it as I do at the end.
>
> How can I solve this problem after the energy minimization ?

You're saying that your energy minimization does not produce a trajectory
(a .trr or .xtc file)?

If that's the case, you just have to instruct GROMACS to periodically
write to a trajectory file using options in the .mdp file (namely,
nstxout). Take a look at:

http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html

Under the section "output control" you will find what you are looking for.

- John

>
> Thanks,
> Mohamed
> --
> 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.
>




John Whittaker
Ph.D. Candidate
Department of Mathematics and Computer Science
Freie Universität Berlin

+49 0160 936 04221

-- 
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.

Re: [gmx-users] pbc nojump with replica exchange behaves differently than with regular MD

[Justin Lemkul]

On 11/28/19 11:04 AM, Ramon Crehuet wrote:

Dear Justin,
Thanks for your suggestion. It works, as long as I set a tpr file in the -s 
option. So this works:

gmx trjconv -f md.trr -s md.tpr -pbc mol -center -o whole.xtc

But the following does not work (where whole_center.gro is a system without 
water molecules with a whole centered protein and some ions):

gmx trjconv -f md.xtc -s whole_center.gro -pbc mol -center -o whole.xtc

I understand that this is what this warning explains:

WARNING: If there are molecules in the input trajectory file
that are broken across periodic boundaries, they
cannot be made whole (or treated as whole) without
you providing a run input file.

This would seem anecdotal, but the problem is that I saved only the non-water 
system in the md.xtc. Therefore the first line works if I select to output only 
the protein atoms, but it gives the following error if I want the non-water 
atoms as output (protein + ions, all that is in the md.xtc).

Fatal error:
Index[413] 36378 is larger than the number of atoms in the
trajectory file (433). There is a mismatch in the contents
of your -f, -s and/or -n files.

Again, this makes sense, as the ions are stored after the water molecules.But I 
am stuck with this two options.
So my question is whether is there is a way to use the tpr for a xtc trajectory 
that contains fewer atoms than the ones defined in the tpr? Or another 
workaround?


Use convert-tpr to make a new .tpr file that matches the contents of the 
.xtc file.


-Justin


Thanks,

Ramon

On 11/28/19 9:44 AM, Ramon Crehuet wrote:

Dear all,
As a follow-up to my question, I have seen that in a regular MD, the 
coordinates of the original trajectory are always smaller than the unitcell 
vectors, whereas this is not true in the trajectory from the replica exchange 
(deviations up to 1.5%). Could this be confusing trajconv?
Could it be that in an exchange attempt only the coordinates of the atoms are 
exchanged between temperatures but not the box size? (the dynamics use a 
Parrinello-Rahman barostat).

The entire state is exchanged (at least in the current version of the
code that I'm looking at), so the box and everything else gets swapped.

For a simple system of solute in water, you should be able to just do
trjconv -pbc mol -center without all the intermediate steps (-pbc whole,
-pbc nojump, etc). I suspect -pbc nojump won't work because you do not
have a continuous trajectory during REMD, so the coordinates may change
quite dramatically between snapshots, leading to a breakdown in the
algorithm.

-Justin


Thanks again.
All the best,
Ramon

- On 28 Nov, 2019, at 11:49, Ramon Crehuet < ramon.crehuet at iqac.csic.es 
> wrote:


Dear all,
I have run a temperature replica exchange and I would like to analyze the
resulting trajectory for a given temperature (i.e. not following a replica
across temperatures using demux.pl).
The simulations consist of a single protein chain. I can easily generate have a
whole molecule, named `whole.pdb`.
When I was running regular MD, the following worked fine to generate whole
structures that diffused out of the box:
gmx trjconv -f md.xtc -s whole.pdb -pbc nojump -o whole.xtc
But repeating that for one of the md.xtc of the replica exchange does not work.
Each atom diffuses or of the box (i.e. without jumps) but to different
directions, resulting in an apparently exploding molecule.
Should there be a different treatment of RE simulations? If so, what should I
do? (I have tried the -pbc nojump step followed or preceded by -pbc whole
without success).
Thanks for your attention.
Best,
Ramon


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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.

Re: [gmx-users] pbc nojump with replica exchange behaves differently than with regular MD

[Ramon Crehuet]

Dear Justin, 
Thanks for your suggestion. It works, as long as I set a tpr file in the -s 
option. So this works: 

gmx trjconv -f md.trr -s md.tpr -pbc mol -center -o whole.xtc 

But the following does not work (where whole_center.gro is a system without 
water molecules with a whole centered protein and some ions): 

gmx trjconv -f md.xtc -s whole_center.gro -pbc mol -center -o whole.xtc 

I understand that this is what this warning explains: 

WARNING: If there are molecules in the input trajectory file 
that are broken across periodic boundaries, they 
cannot be made whole (or treated as whole) without 
you providing a run input file. 

This would seem anecdotal, but the problem is that I saved only the non-water 
system in the md.xtc. Therefore the first line works if I select to output only 
the protein atoms, but it gives the following error if I want the non-water 
atoms as output (protein + ions, all that is in the md.xtc). 

Fatal error: 
Index[413] 36378 is larger than the number of atoms in the 
trajectory file (433). There is a mismatch in the contents 
of your -f, -s and/or -n files. 

Again, this makes sense, as the ions are stored after the water molecules.But I 
am stuck with this two options. 
So my question is whether is there is a way to use the tpr for a xtc trajectory 
that contains fewer atoms than the ones defined in the tpr? Or another 
workaround? 

Thanks, 

Ramon 

On 11/28/19 9:44 AM, Ramon Crehuet wrote:
> Dear all,
> As a follow-up to my question, I have seen that in a regular MD, the 
> coordinates of the original trajectory are always smaller than the unitcell 
> vectors, whereas this is not true in the trajectory from the replica exchange 
> (deviations up to 1.5%). Could this be confusing trajconv?
> Could it be that in an exchange attempt only the coordinates of the atoms are 
> exchanged between temperatures but not the box size? (the dynamics use a 
> Parrinello-Rahman barostat).

The entire state is exchanged (at least in the current version of the 
code that I'm looking at), so the box and everything else gets swapped.

For a simple system of solute in water, you should be able to just do 
trjconv -pbc mol -center without all the intermediate steps (-pbc whole, 
-pbc nojump, etc). I suspect -pbc nojump won't work because you do not 
have a continuous trajectory during REMD, so the coordinates may change 
quite dramatically between snapshots, leading to a breakdown in the 
algorithm.

-Justin

> Thanks again.
> All the best,
> Ramon
>
> - On 28 Nov, 2019, at 11:49, Ramon Crehuet < ramon.crehuet at 
> iqac.csic.es > wrote:
>
>> Dear all,
>> I have run a temperature replica exchange and I would like to analyze the
>> resulting trajectory for a given temperature (i.e. not following a replica
>> across temperatures using demux.pl).
>> The simulations consist of a single protein chain. I can easily generate 
>> have a
>> whole molecule, named `whole.pdb`.
>> When I was running regular MD, the following worked fine to generate whole
>> structures that diffused out of the box:
>> gmx trjconv -f md.xtc -s whole.pdb -pbc nojump -o whole.xtc
>> But repeating that for one of the md.xtc of the replica exchange does not 
>> work.
>> Each atom diffuses or of the box (i.e. without jumps) but to different
>> directions, resulting in an apparently exploding molecule.
>> Should there be a different treatment of RE simulations? If so, what should I
>> do? (I have tried the -pbc nojump step followed or preceded by -pbc whole
>> without success).
>> Thanks for your attention.
>> Best,
>> Ramon

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 
http://www.thelemkullab.com == 
-- 
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.

Re: [gmx-users] pbc nojump with replica exchange behaves differently than with regular MD

[Justin Lemkul]

On 11/28/19 9:44 AM, Ramon Crehuet wrote:

Dear all,
As a follow-up to my question, I have seen that in a regular MD, the 
coordinates of the original trajectory are always smaller than the unitcell 
vectors, whereas this is not true in the trajectory from the replica exchange 
(deviations up to 1.5%). Could this be confusing trajconv?
Could it be that in an exchange attempt only the coordinates of the atoms are 
exchanged between temperatures but not the box size? (the dynamics use a 
Parrinello-Rahman barostat).


The entire state is exchanged (at least in the current version of the 
code that I'm looking at), so the box and everything else gets swapped.


For a simple system of solute in water, you should be able to just do 
trjconv -pbc mol -center without all the intermediate steps (-pbc whole, 
-pbc nojump, etc). I suspect -pbc nojump won't work because you do not 
have a continuous trajectory during REMD, so the coordinates may change 
quite dramatically between snapshots, leading to a breakdown in the 
algorithm.


-Justin


Thanks again.
All the best,
Ramon

- On 28 Nov, 2019, at 11:49, Ramon Crehuet  
wrote:


Dear all,
I have run a temperature replica exchange and I would like to analyze the
resulting trajectory for a given temperature (i.e. not following a replica
across temperatures using demux.pl).
The simulations consist of a single protein chain. I can easily generate have a
whole molecule, named `whole.pdb`.
When I was running regular MD, the following worked fine to generate whole
structures that diffused out of the box:
gmx trjconv -f md.xtc -s whole.pdb -pbc nojump -o whole.xtc
But repeating that for one of the md.xtc of the replica exchange does not work.
Each atom diffuses or of the box (i.e. without jumps) but to different
directions, resulting in an apparently exploding molecule.
Should there be a different treatment of RE simulations? If so, what should I
do? (I have tried the -pbc nojump step followed or preceded by -pbc whole
without success).
Thanks for your attention.
Best,
Ramon


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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.

Re: [gmx-users] pbc nojump with replica exchange behaves differently than with regular MD

[Ramon Crehuet]

Dear all, 
As a follow-up to my question, I have seen that in a regular MD, the 
coordinates of the original trajectory are always smaller than the unitcell 
vectors, whereas this is not true in the trajectory from the replica exchange 
(deviations up to 1.5%). Could this be confusing trajconv? 
Could it be that in an exchange attempt only the coordinates of the atoms are 
exchanged between temperatures but not the box size? (the dynamics use a 
Parrinello-Rahman barostat). 
Thanks again. 
All the best, 
Ramon 

- On 28 Nov, 2019, at 11:49, Ramon Crehuet  
wrote: 

> Dear all,
> I have run a temperature replica exchange and I would like to analyze the
> resulting trajectory for a given temperature (i.e. not following a replica
> across temperatures using demux.pl).
> The simulations consist of a single protein chain. I can easily generate have 
> a
> whole molecule, named `whole.pdb`.
> When I was running regular MD, the following worked fine to generate whole
> structures that diffused out of the box:

> gmx trjconv -f md.xtc -s whole.pdb -pbc nojump -o whole.xtc

> But repeating that for one of the md.xtc of the replica exchange does not 
> work.
> Each atom diffuses or of the box (i.e. without jumps) but to different
> directions, resulting in an apparently exploding molecule.
> Should there be a different treatment of RE simulations? If so, what should I
> do? (I have tried the -pbc nojump step followed or preceded by -pbc whole
> without success).
> Thanks for your attention.
> Best,
> Ramon
-- 
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.

Re: [gmx-users] PBC conditions for Vacuum simulation

[Mark Abraham]

Hi,

No. Models without cutoffs will scale badly with particle count. Adding
cutoffs is not always a performance win either, because while that saves
computation of interactions, it adds the need to periodically search for
which particle interactions to compute.

Mark

On Sat., 9 Feb. 2019, 17:24 Neena Susan Eappen, <
neena.susaneap...@mail.utoronto.ca> wrote:

> Hello gromacs users,
>
> I am trying to model a peptide in gas phase which requires proper
> conditions like: no PBC, no cut-offs for VanderWaals and electrostatics,
> coulomb type not PME. However, this increases computational time by N^2 for
> N number of atoms. Is there a way to mitigate this?
>
> Many thanks,
> Neena
>
> --
> 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
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] PBC fix for visualization

[Mohsen Ramezanpour]

Hi Dallas and other Gromacs users,

I used -pbc whole and -ur compact in the first step
"System" index group

And then, used the output file for -pbc cluster.
Choosing the "System" index for clustering gave the best result I got.
(Although there are still few lipids which are not completely in the places
they should be).

Anyway, the outputs are reasonable. However, I have ca. 100 simulation
systems each of ca. 500 ns. (each system composed of ca. 4000 molecules)
Doing this clustering on the whole system takes a considerable time.

I thought I might be able to do the clustering on a group of atoms (an
index group composed of P in lipids and O in water molecules).
This, however, did not work and gmx trjconv complained about:

"Molecule 1 marked for clustering but not atom 1 in it - check your index!"

I was wondering what would be your solution to this?

Cheers,
Mohsen

On Mon, May 22, 2017 at 11:45 AM, Mohsen Ramezanpour <
ramezanpour.moh...@gmail.com> wrote:

> Hi Dallas,
>
> Thanks for your reply.
> I did try -pbc cluster for waters. It could fix it somehow but not
> completely.
> After that, I had to use -pbc center to fix it. Still, I do not get what I
> want.
> Unfortunately, some waters and lipids are appearing from the other side of
> the box.
>
> Cheers,
> Mohsen
>
>
> On Sun, May 21, 2017 at 8:12 PM, Dallas Warren 
> wrote:
>
>> I have found the cluster option of -pbc to work well for putting
>> aggregates back together correctly. Some times you do need an index
>> file and appropriate groups to assist with it getting it right.
>>
>> gmx trjconv -pbc cluster
>> Catch ya,
>>
>> Dr. Dallas Warren
>> Drug Delivery, Disposition and Dynamics
>> Monash Institute of Pharmaceutical Sciences, Monash University
>> 381 Royal Parade, Parkville VIC 3052
>> dallas.war...@monash.edu
>> -
>> When the only tool you own is a hammer, every problem begins to resemble
>> a nail.
>>
>>
>> On 16 May 2017 at 07:50, Mohsen Ramezanpour
>>  wrote:
>> > Dear Gromacs users,
>> >
>> > I have an HII phase made of one inverted cylinder (and waters inside)
>> in a
>> > triclinic box with 90, 90, 60 angles. After running the simulation, this
>> > cylinder become bent like a curve. I.e. is not a perfect cylinder
>> anymore.
>> > As a result, some water molecules and lipids pass the box sides and
>> enter
>> > from the other side of box because of PBC.
>> > Now, I want to make the cylinder again but I am not sure how to do so.
>> >
>> > The best I could do was to use "-pbc mol  -ur compact" options in
>> trjconv.
>> > However, here are still some lipids and molecules which are not part of
>> the
>> > cylinder.
>> >
>> > Any idea how could I fix the effect of these PBC in visualization?
>> >
>> > Thanks
>> > Mohsen
>> >
>> > --
>> > *Rewards work better than punishment ...*
>> > --
>> > 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
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
>
> --
> *Rewards work better than punishment ...*
>



-- 
*Rewards work better than punishment ...*
-- 
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.

Re: [gmx-users] PBC

[Justin Lemkul]

On 2/12/18 8:44 AM, Ahmed Mashaly wrote:

Hi
If I want to use gmx trjconv to recenter the protein in xtc file, the reference 
(-s) .tpr should be the one I used in simulation (md.tpr) or I can use the 
first one (em.tpr) without a difference?

This is because the protein has jumped after em step, and if I have to use 
md.tpr as reference for md.xtc, I will have to recenter it after every step of 
em, nvt, npt


You can use whatever reference coordinates you want. Energy minimization 
generally shouldn't result in large structural changes, so make sure you 
have a sufficiently large box to avoid spurious minimum image interactions.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
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.

Re: [gmx-users] Pbc

[Justin Lemkul]

On 8/16/17 4:24 PM, farial tavakoli wrote:

  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear gromacs users
I need to visualize my md_0_1.tpr , so i issued  trjconv -s md_0_1.tpr -f 
md_0_1.xtc -o xxx.pdb -pbc nojump -dt 10to remove the jumps over the boundaries 
and make a continuous trajectoryPBCBut when i visualized my complex by pymol, 
the protein appeared broken . Would you please help me to solve it?


The molecules are broken because you didn't tell trjconv to make them 
whole.  Google is your friend... 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
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.

Re: [gmx-users] PBC ISSUES IN GROMACS

[Mark Abraham]

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
had useful information

Mark

On Mon, 14 Aug 2017 09:17 Neha Gupta  wrote:

> Hi gromacs users,
>
> After simulation for 5 ns, I generated a movie.pdb file using .gro and .xtc
>
> However, in the movie file, I witnessed bizarre long bonds...
>
> How to fix it?
>
> Any suggestions please?
>
>
> Thanks,
> Neha
> --
> 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
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] PBC ISSUES IN GROMACS

[David van der Spoel]

On 14/08/17 09:17, Neha Gupta wrote:

Hi gromacs users,

After simulation for 5 ns, I generated a movie.pdb file using .gro and .xtc

However, in the movie file, I witnessed bizarre long bonds...

How to fix it?

Any suggestions please?

trjconv -pbc whole



Thanks,
Neha




--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
--
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.

Re: [gmx-users] PBC fix for visualization

[Mohsen Ramezanpour]

Hi Dallas,

Thanks for your reply.
I did try -pbc cluster for waters. It could fix it somehow but not
completely.
After that, I had to use -pbc center to fix it. Still, I do not get what I
want.
Unfortunately, some waters and lipids are appearing from the other side of
the box.

Cheers,
Mohsen


On Sun, May 21, 2017 at 8:12 PM, Dallas Warren 
wrote:

> I have found the cluster option of -pbc to work well for putting
> aggregates back together correctly. Some times you do need an index
> file and appropriate groups to assist with it getting it right.
>
> gmx trjconv -pbc cluster
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.war...@monash.edu
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On 16 May 2017 at 07:50, Mohsen Ramezanpour
>  wrote:
> > Dear Gromacs users,
> >
> > I have an HII phase made of one inverted cylinder (and waters inside) in
> a
> > triclinic box with 90, 90, 60 angles. After running the simulation, this
> > cylinder become bent like a curve. I.e. is not a perfect cylinder
> anymore.
> > As a result, some water molecules and lipids pass the box sides and enter
> > from the other side of box because of PBC.
> > Now, I want to make the cylinder again but I am not sure how to do so.
> >
> > The best I could do was to use "-pbc mol  -ur compact" options in
> trjconv.
> > However, here are still some lipids and molecules which are not part of
> the
> > cylinder.
> >
> > Any idea how could I fix the effect of these PBC in visualization?
> >
> > Thanks
> > Mohsen
> >
> > --
> > *Rewards work better than punishment ...*
> > --
> > 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
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
*Rewards work better than punishment ...*
-- 
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.

Re: [gmx-users] PBC fix for visualization

[Dallas Warren]

I have found the cluster option of -pbc to work well for putting
aggregates back together correctly. Some times you do need an index
file and appropriate groups to assist with it getting it right.

gmx trjconv -pbc cluster
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 16 May 2017 at 07:50, Mohsen Ramezanpour
 wrote:
> Dear Gromacs users,
>
> I have an HII phase made of one inverted cylinder (and waters inside) in a
> triclinic box with 90, 90, 60 angles. After running the simulation, this
> cylinder become bent like a curve. I.e. is not a perfect cylinder anymore.
> As a result, some water molecules and lipids pass the box sides and enter
> from the other side of box because of PBC.
> Now, I want to make the cylinder again but I am not sure how to do so.
>
> The best I could do was to use "-pbc mol  -ur compact" options in trjconv.
> However, here are still some lipids and molecules which are not part of the
> cylinder.
>
> Any idea how could I fix the effect of these PBC in visualization?
>
> Thanks
> Mohsen
>
> --
> *Rewards work better than punishment ...*
> --
> 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
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] PBC

[Justin Lemkul]

On 5/5/17 1:37 PM, Alex wrote:

Dear Gromacs user,

I want to study the interaction between a nanoparticle(5 nm diameter) and
some heptapeptide around the nanoparticle in aqueous solution. I put
the nanoparticle
in the center of a box and the rest are around it.
I was wondering if I should use PBC (periodic boundary condition) in such a
system? What is the advantage of the using PBC here?



The same as any system - you don't have boundary effects and your system won't 
turn into a quickly evaporating droplet.


-Justin


The disadvantage of using PBC here is that a very big box should be used to
avoid interaction between a peptide and another peptide in the adjacent
cell.

Regards,
Alex



--
==

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.

Re: [gmx-users] PBC issues with membrane-peptide simulation

[Abhi Acharya]

Dear users,

Well, I have found another solution for avoiding the diffusion through the
periodic boundary in such simulations. Hope this is helpful to others doing
similar work.

Basically, the idea is to apply a biasing potential to the COM of the
peptides to pull them towards the membrane so as to ensure interaction with
the lipid bilayer. Thereafter, normal production simulations can be
performed on the peptide membrane complex. See the following paper:

Li, J., Liu, S., Lakshminarayanan, R., Bai, Y., Pervushin, K., Verma, C.,
and Beuerman, R.W. (2013). Molecular simulations suggest how a branched
antimicrobial peptide perturbs a bacterial membrane and enhances
permeability. Biochim. Biophys. Acta *1828*, 1112–1121.

Best Regards,
Abhishek Acharya



On Thu, Nov 10, 2016 at 12:48 PM, Abhi Acharya 
wrote:

> Sorry for that Mark.
>
> Basically, our experimental studies show that our designed peptides (2-3
> different peptides)  are involved in membrane destabilization but their
> activity (in terms of MIC values) varies. We want to understand the
> molecular underpinnings of the membrane destabilization process and
> possibly explain the variation in activities of the peptides. Therefore, we
> wanted to perform some simulations starting from the point where some
> amount of peptides are randomly added to the simulation box on one side of
> the membrane (about 5 nm away from the upper leaflet) and see how the
> system evolves.
>
> The problem is that some of the peptides diffuse along the z-direction
> such that they exit the simulation box and appear on the other side near to
> the lower leaflet.
>
> Hope this is helpful.
>
> Thanks and Regards,
> Abhishek Acharya
>
>
>
>
>
> On Thu, Nov 10, 2016 at 9:57 AM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> You haven't said what you're trying to model, so it's going to be hard for
>> someone to help out :-)
>>
>> Mark
>>
>> On Thu, 10 Nov 2016 05:21 Abhi Acharya  wrote:
>>
>> > Thank you Stephane for your suggestion. Though this seems like a nice
>> > solution to circumvent the problem, but do you think this is the normal
>> way
>> > to go about it? I have never found anyone reporting such a methodology
>> for
>> > membrane peptide simulation. Also, I can anticipate significant
>> increase in
>> > computational costs for a double bilayer system. I have a 800 lipid
>> > molecules in a single bilayer, so this is significant factor for me.
>> >
>> > Thanks and Regards,
>> > Abhishek
>> >
>> > On Wed, Nov 9, 2016 at 4:53 PM, ABEL Stephane 175950 <
>> stephane.a...@cea.fr
>> > >
>> > wrote:
>> >
>> > > Hi,
>> > >
>> > > it is not an issue !! To resolve your problem you could simulate two
>> > > bilayer in box and  insert the peptides between them.
>> > >
>> > > HTH
>> > >
>> > > --
>> > >
>> > > Message: 6
>> > > Date: Wed, 9 Nov 2016 16:07:26 +0530
>> > > From: Abhi Acharya 
>> > > To: gromacs.org_gmx-users@maillist.sys.kth.se
>> > > Subject: [gmx-users] Fwd: PBC issues with membrane-peptide simulation
>> > > Message-ID:
>> > > > > > gmail.com>
>> > > Content-Type: text/plain; charset=UTF-8
>> > >
>> > > Dear Gromacs users,
>> > >
>> > > I am trying to simulate a system consisting of a lipid bilayer and few
>> > > peptides. The peptides have been added randomly to the simulation box
>> > only
>> > > on one side of the membrane. I ran a 100 ns simulation of the system
>> > using
>> > > CHARMM36 forcefeild. However, I find that within the first few ns,
>> some
>> > of
>> > > the peptides appear on the other side of the membrane. I think that
>> this
>> > is
>> > > because of the diffusion of the peptides though the periodic boundary.
>> > > Kindly suggest  how to tackle this problem. I have used COM motion
>> > removal
>> > > on the whole system for the said simulation.
>> > >
>> > > Regards,
>> > > Abhishek Acharya
>> > >
>> > >
>> > > --
>> > >
>> > > --
>> > > 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.
>> > >
>> > > End of gromacs.org_gmx-users Digest, Vol 151, Issue 32
>> > > **
>> > > --
>> > > 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
>> > > 

Re: [gmx-users] PBC issues with membrane-peptide simulation

[Abhi Acharya]

Sorry for that Mark.

Basically, our experimental studies show that our designed peptides (2-3
different peptides)  are involved in membrane destabilization but their
activity (in terms of MIC values) varies. We want to understand the
molecular underpinnings of the membrane destabilization process and
possibly explain the variation in activities of the peptides. Therefore, we
wanted to perform some simulations starting from the point where some
amount of peptides are randomly added to the simulation box on one side of
the membrane (about 5 nm away from the upper leaflet) and see how the
system evolves.

The problem is that some of the peptides diffuse along the z-direction such
that they exit the simulation box and appear on the other side near to the
lower leaflet.

Hope this is helpful.

Thanks and Regards,
Abhishek Acharya





On Thu, Nov 10, 2016 at 9:57 AM, Mark Abraham 
wrote:

> Hi,
>
> You haven't said what you're trying to model, so it's going to be hard for
> someone to help out :-)
>
> Mark
>
> On Thu, 10 Nov 2016 05:21 Abhi Acharya  wrote:
>
> > Thank you Stephane for your suggestion. Though this seems like a nice
> > solution to circumvent the problem, but do you think this is the normal
> way
> > to go about it? I have never found anyone reporting such a methodology
> for
> > membrane peptide simulation. Also, I can anticipate significant increase
> in
> > computational costs for a double bilayer system. I have a 800 lipid
> > molecules in a single bilayer, so this is significant factor for me.
> >
> > Thanks and Regards,
> > Abhishek
> >
> > On Wed, Nov 9, 2016 at 4:53 PM, ABEL Stephane 175950 <
> stephane.a...@cea.fr
> > >
> > wrote:
> >
> > > Hi,
> > >
> > > it is not an issue !! To resolve your problem you could simulate two
> > > bilayer in box and  insert the peptides between them.
> > >
> > > HTH
> > >
> > > --
> > >
> > > Message: 6
> > > Date: Wed, 9 Nov 2016 16:07:26 +0530
> > > From: Abhi Acharya 
> > > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > > Subject: [gmx-users] Fwd: PBC issues with membrane-peptide simulation
> > > Message-ID:
> > >  > > gmail.com>
> > > Content-Type: text/plain; charset=UTF-8
> > >
> > > Dear Gromacs users,
> > >
> > > I am trying to simulate a system consisting of a lipid bilayer and few
> > > peptides. The peptides have been added randomly to the simulation box
> > only
> > > on one side of the membrane. I ran a 100 ns simulation of the system
> > using
> > > CHARMM36 forcefeild. However, I find that within the first few ns, some
> > of
> > > the peptides appear on the other side of the membrane. I think that
> this
> > is
> > > because of the diffusion of the peptides though the periodic boundary.
> > > Kindly suggest  how to tackle this problem. I have used COM motion
> > removal
> > > on the whole system for the said simulation.
> > >
> > > Regards,
> > > Abhishek Acharya
> > >
> > >
> > > --
> > >
> > > --
> > > 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.
> > >
> > > End of gromacs.org_gmx-users Digest, Vol 151, Issue 32
> > > **
> > > --
> > > 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
> > 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
> 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 

Re: [gmx-users] PBC issues with membrane-peptide simulation

[Mark Abraham]

Hi,

You haven't said what you're trying to model, so it's going to be hard for
someone to help out :-)

Mark

On Thu, 10 Nov 2016 05:21 Abhi Acharya  wrote:

> Thank you Stephane for your suggestion. Though this seems like a nice
> solution to circumvent the problem, but do you think this is the normal way
> to go about it? I have never found anyone reporting such a methodology for
> membrane peptide simulation. Also, I can anticipate significant increase in
> computational costs for a double bilayer system. I have a 800 lipid
> molecules in a single bilayer, so this is significant factor for me.
>
> Thanks and Regards,
> Abhishek
>
> On Wed, Nov 9, 2016 at 4:53 PM, ABEL Stephane 175950  >
> wrote:
>
> > Hi,
> >
> > it is not an issue !! To resolve your problem you could simulate two
> > bilayer in box and  insert the peptides between them.
> >
> > HTH
> >
> > --
> >
> > Message: 6
> > Date: Wed, 9 Nov 2016 16:07:26 +0530
> > From: Abhi Acharya 
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: [gmx-users] Fwd: PBC issues with membrane-peptide simulation
> > Message-ID:
> >  > gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Dear Gromacs users,
> >
> > I am trying to simulate a system consisting of a lipid bilayer and few
> > peptides. The peptides have been added randomly to the simulation box
> only
> > on one side of the membrane. I ran a 100 ns simulation of the system
> using
> > CHARMM36 forcefeild. However, I find that within the first few ns, some
> of
> > the peptides appear on the other side of the membrane. I think that this
> is
> > because of the diffusion of the peptides though the periodic boundary.
> > Kindly suggest  how to tackle this problem. I have used COM motion
> removal
> > on the whole system for the said simulation.
> >
> > Regards,
> > Abhishek Acharya
> >
> >
> > --
> >
> > --
> > 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.
> >
> > End of gromacs.org_gmx-users Digest, Vol 151, Issue 32
> > **
> > --
> > 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
> 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
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] PBC issues with membrane-peptide simulation

[Abhi Acharya]

Thank you Stephane for your suggestion. Though this seems like a nice
solution to circumvent the problem, but do you think this is the normal way
to go about it? I have never found anyone reporting such a methodology for
membrane peptide simulation. Also, I can anticipate significant increase in
computational costs for a double bilayer system. I have a 800 lipid
molecules in a single bilayer, so this is significant factor for me.

Thanks and Regards,
Abhishek

On Wed, Nov 9, 2016 at 4:53 PM, ABEL Stephane 175950 
wrote:

> Hi,
>
> it is not an issue !! To resolve your problem you could simulate two
> bilayer in box and  insert the peptides between them.
>
> HTH
>
> --
>
> Message: 6
> Date: Wed, 9 Nov 2016 16:07:26 +0530
> From: Abhi Acharya 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Fwd: PBC issues with membrane-peptide simulation
> Message-ID:
>  gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Gromacs users,
>
> I am trying to simulate a system consisting of a lipid bilayer and few
> peptides. The peptides have been added randomly to the simulation box only
> on one side of the membrane. I ran a 100 ns simulation of the system using
> CHARMM36 forcefeild. However, I find that within the first few ns, some of
> the peptides appear on the other side of the membrane. I think that this is
> because of the diffusion of the peptides though the periodic boundary.
> Kindly suggest  how to tackle this problem. I have used COM motion removal
> on the whole system for the said simulation.
>
> Regards,
> Abhishek Acharya
>
>
> --
>
> --
> 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.
>
> End of gromacs.org_gmx-users Digest, Vol 151, Issue 32
> **
> --
> 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
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] -pbc nojump failure

[Erik Marklund]

Dear Irem,

You may want to run the trajectory through trjconv and translate it, or use 
e.g. -pbc whole, so that the protein is intact at frame 1. Then you can run 
trjconv -pbc nojump on the resulting trajectory. This usually requires a bit of 
trial and error.

Kind regards,
Erik

> On 31 Mar 2016, at 18:36, Irem Altan  wrote:
> 
> I think the problem is that I can’t seem to start from an unfragmented 
> structure. I start from the .pdb file, where the protein is a whole, and end 
> up with a .tpr file that is fragmented. The interesting thing is, this did 
> not happen with version 4.6.5 (I now use 5.1.2). Do I have to do something 
> extra while preparing the simulation system? 
> 
> Here is what I’m currently doing:
> 
> gmx pdb2gmx -f .pdb -o box.gro -p topol.top (then I choose 
> amber99sb and tip4pew)
> gmx solvate -cp box.gro -cs tip4p -p topol.top -o box_h2o.gro
> gmx grompp -f ions.mdp -c box_h2o.gro -o ions.tpr -p topol.top
> gmx genion -s ions.tpr -p topol.top -o ions.gro -neutral -conc 0.05  (I 
> choose to replace the solvation waters, SOL)
> gmx -f minim.mdp -p topol.top -c ions.gro -o em.tpr
> gmx mdrun -v -deffnm em
> gmx grompp -f nvt.mdp -p topol.top -c em.gro -o nvt_water_frozen.tpr
> 
> Then I run the simulation with mdrun. The .mdp files are almost identical to 
> Justin’s files from the Lysozyme tutorial. In the above steps, is there 
> something that seems like it could cause the fragmentation issue? 
> 
> Best,
> Irem
> 
>> On Mar 31, 2016, at 11:54 AM, Tsjerk Wassenaar  wrote:
>> 
>> No! You can't do that, because fitting will cause the PBC and the
>> coordinates to mismatch. So 'nojump' after that will for sure screw up the
>> coordinates. Check the trjconv workflow on the Gromacs site.
>> 
>> Cheers,
>> 
>> Tsjerk
>> On Mar 31, 2016 14:23, "Francesco Carbone"  wrote:
>> 
>>> You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump)
>>> later.
>>> 
>>> Cheers,
>>> 
>>> Fra
>>> 
>>> On 31 March 2016 at 05:45, Tsjerk Wassenaar  wrote:
>>> 
 Hi Irem,
 
 Check the structure in nvt_water_frozen.tpr:
 
 gmx editconf -f nvt_water_frozen.tpr -o ref.pdb
 
 Cheers,
 
 Tsjerk
 On Mar 31, 2016 00:04, "Irem Altan"  wrote:
 
> Hi,
> 
> I am simulating a protein in its unit cell. I use the original .pdb
>>> file
> as an input, so the initial molecule is not fragmented. At the end of
>>> the
> simulation, I generate a .pdb file containing the trajectory of the
 protein
> as follows:
> 
> gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc
> nojump -o prot.pdb
> 
> Despite the fact that I use -pbc nojump, I still get all the
>>> coordinates
> wrapped into the unit cell, and therefore the protein fragmented. What
> could be wrong? (I use GROMACS 5.1.2)
> 
> Best,
> Irem
> --
> 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
 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
>>> 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
>> 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
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
> mail to 

Re: [gmx-users] -pbc nojump failure

[Irem Altan]

I think the problem is that I can’t seem to start from an unfragmented 
structure. I start from the .pdb file, where the protein is a whole, and end up 
with a .tpr file that is fragmented. The interesting thing is, this did not 
happen with version 4.6.5 (I now use 5.1.2). Do I have to do something extra 
while preparing the simulation system? 

Here is what I’m currently doing:

gmx pdb2gmx -f .pdb -o box.gro -p topol.top (then I choose 
amber99sb and tip4pew)
gmx solvate -cp box.gro -cs tip4p -p topol.top -o box_h2o.gro
gmx grompp -f ions.mdp -c box_h2o.gro -o ions.tpr -p topol.top
gmx genion -s ions.tpr -p topol.top -o ions.gro -neutral -conc 0.05  (I choose 
to replace the solvation waters, SOL)
gmx -f minim.mdp -p topol.top -c ions.gro -o em.tpr
gmx mdrun -v -deffnm em
gmx grompp -f nvt.mdp -p topol.top -c em.gro -o nvt_water_frozen.tpr

Then I run the simulation with mdrun. The .mdp files are almost identical to 
Justin’s files from the Lysozyme tutorial. In the above steps, is there 
something that seems like it could cause the fragmentation issue? 

Best,
Irem

> On Mar 31, 2016, at 11:54 AM, Tsjerk Wassenaar  wrote:
> 
> No! You can't do that, because fitting will cause the PBC and the
> coordinates to mismatch. So 'nojump' after that will for sure screw up the
> coordinates. Check the trjconv workflow on the Gromacs site.
> 
> Cheers,
> 
> Tsjerk
> On Mar 31, 2016 14:23, "Francesco Carbone"  wrote:
> 
>> You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump)
>> later.
>> 
>> Cheers,
>> 
>> Fra
>> 
>> On 31 March 2016 at 05:45, Tsjerk Wassenaar  wrote:
>> 
>>> Hi Irem,
>>> 
>>> Check the structure in nvt_water_frozen.tpr:
>>> 
>>> gmx editconf -f nvt_water_frozen.tpr -o ref.pdb
>>> 
>>> Cheers,
>>> 
>>> Tsjerk
>>> On Mar 31, 2016 00:04, "Irem Altan"  wrote:
>>> 
 Hi,
 
 I am simulating a protein in its unit cell. I use the original .pdb
>> file
 as an input, so the initial molecule is not fragmented. At the end of
>> the
 simulation, I generate a .pdb file containing the trajectory of the
>>> protein
 as follows:
 
 gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc
 nojump -o prot.pdb
 
 Despite the fact that I use -pbc nojump, I still get all the
>> coordinates
 wrapped into the unit cell, and therefore the protein fragmented. What
 could be wrong? (I use GROMACS 5.1.2)
 
 Best,
 Irem
 --
 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
>>> 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
>> 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
> 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
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] -pbc nojump failure

[Tsjerk Wassenaar]

No! You can't do that, because fitting will cause the PBC and the
coordinates to mismatch. So 'nojump' after that will for sure screw up the
coordinates. Check the trjconv workflow on the Gromacs site.

Cheers,

Tsjerk
On Mar 31, 2016 14:23, "Francesco Carbone"  wrote:

> You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump)
> later.
>
> Cheers,
>
> Fra
>
> On 31 March 2016 at 05:45, Tsjerk Wassenaar  wrote:
>
> > Hi Irem,
> >
> > Check the structure in nvt_water_frozen.tpr:
> >
> > gmx editconf -f nvt_water_frozen.tpr -o ref.pdb
> >
> > Cheers,
> >
> > Tsjerk
> > On Mar 31, 2016 00:04, "Irem Altan"  wrote:
> >
> > > Hi,
> > >
> > > I am simulating a protein in its unit cell. I use the original .pdb
> file
> > > as an input, so the initial molecule is not fragmented. At the end of
> the
> > > simulation, I generate a .pdb file containing the trajectory of the
> > protein
> > > as follows:
> > >
> > > gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc
> > > nojump -o prot.pdb
> > >
> > > Despite the fact that I use -pbc nojump, I still get all the
> coordinates
> > > wrapped into the unit cell, and therefore the protein fragmented. What
> > > could be wrong? (I use GROMACS 5.1.2)
> > >
> > > Best,
> > > Irem
> > > --
> > > 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
> > 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
> 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
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] -pbc nojump failure

[Irem Altan]

Hi,

Thanks. If I do that, the reference structure would be what’s in the .tpr file, 
right?

Best,
Irem

> On Mar 31, 2016, at 8:22 AM, Francesco Carbone  wrote:
> 
> You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump) later.
> 
> Cheers,
> 
> Fra
> 
> On 31 March 2016 at 05:45, Tsjerk Wassenaar  wrote:
> 
>> Hi Irem,
>> 
>> Check the structure in nvt_water_frozen.tpr:
>> 
>> gmx editconf -f nvt_water_frozen.tpr -o ref.pdb
>> 
>> Cheers,
>> 
>> Tsjerk
>> On Mar 31, 2016 00:04, "Irem Altan"  wrote:
>> 
>>> Hi,
>>> 
>>> I am simulating a protein in its unit cell. I use the original .pdb file
>>> as an input, so the initial molecule is not fragmented. At the end of the
>>> simulation, I generate a .pdb file containing the trajectory of the
>> protein
>>> as follows:
>>> 
>>> gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc
>>> nojump -o prot.pdb
>>> 
>>> Despite the fact that I use -pbc nojump, I still get all the coordinates
>>> wrapped into the unit cell, and therefore the protein fragmented. What
>>> could be wrong? (I use GROMACS 5.1.2)
>>> 
>>> Best,
>>> Irem
>>> --
>>> 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
>> 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
> 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
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] -pbc nojump failure

[Irem Altan]

Hi,

Thanks for your suggestion. Unsurprisingly, the structure in 
nvt_water_frozen.tpr is also fragmented. Is there a way to use the input .pdb 
file as reference, somehow?

Best,
Irem

> On Mar 31, 2016, at 12:45 AM, Tsjerk Wassenaar  wrote:
> 
> Hi Irem,
> 
> Check the structure in nvt_water_frozen.tpr:
> 
> gmx editconf -f nvt_water_frozen.tpr -o ref.pdb
> 
> Cheers,
> 
> Tsjerk
> On Mar 31, 2016 00:04, "Irem Altan"  wrote:
> 
>> Hi,
>> 
>> I am simulating a protein in its unit cell. I use the original .pdb file
>> as an input, so the initial molecule is not fragmented. At the end of the
>> simulation, I generate a .pdb file containing the trajectory of the protein
>> as follows:
>> 
>> gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc
>> nojump -o prot.pdb
>> 
>> Despite the fact that I use -pbc nojump, I still get all the coordinates
>> wrapped into the unit cell, and therefore the protein fragmented. What
>> could be wrong? (I use GROMACS 5.1.2)
>> 
>> Best,
>> Irem
>> --
>> 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
> 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
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] -pbc nojump failure

[Francesco Carbone]

You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump) later.

Cheers,

Fra

On 31 March 2016 at 05:45, Tsjerk Wassenaar  wrote:

> Hi Irem,
>
> Check the structure in nvt_water_frozen.tpr:
>
> gmx editconf -f nvt_water_frozen.tpr -o ref.pdb
>
> Cheers,
>
> Tsjerk
> On Mar 31, 2016 00:04, "Irem Altan"  wrote:
>
> > Hi,
> >
> > I am simulating a protein in its unit cell. I use the original .pdb file
> > as an input, so the initial molecule is not fragmented. At the end of the
> > simulation, I generate a .pdb file containing the trajectory of the
> protein
> > as follows:
> >
> > gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc
> > nojump -o prot.pdb
> >
> > Despite the fact that I use -pbc nojump, I still get all the coordinates
> > wrapped into the unit cell, and therefore the protein fragmented. What
> > could be wrong? (I use GROMACS 5.1.2)
> >
> > Best,
> > Irem
> > --
> > 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
> 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
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] -pbc nojump failure

[Tsjerk Wassenaar]

Hi Irem,

Check the structure in nvt_water_frozen.tpr:

gmx editconf -f nvt_water_frozen.tpr -o ref.pdb

Cheers,

Tsjerk
On Mar 31, 2016 00:04, "Irem Altan"  wrote:

> Hi,
>
> I am simulating a protein in its unit cell. I use the original .pdb file
> as an input, so the initial molecule is not fragmented. At the end of the
> simulation, I generate a .pdb file containing the trajectory of the protein
> as follows:
>
> gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc
> nojump -o prot.pdb
>
> Despite the fact that I use -pbc nojump, I still get all the coordinates
> wrapped into the unit cell, and therefore the protein fragmented. What
> could be wrong? (I use GROMACS 5.1.2)
>
> Best,
> Irem
> --
> 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
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pbc

[Justin Lemkul]

On 1/5/16 11:58 AM, Parvez Mh wrote:

Dear all:

I am using pbc in all directions, it is expected that,  i will observe
broken molecules in central box. But i am wondering, some molecules are out
of box when i visualize with vmd. What would the right explanation of this?



PBC is the explanation.

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.

Re: [gmx-users] pbc

[Justin Lemkul]

On 10/19/15 9:59 PM, Sana Saeed wrote:

good morning gmx usersi want to visualize the box from my gro file. I am using 
VMD , i read the manual but couldnt understand how to use my own vectors to 
visualize box. actually i want to see if the atoms are out of box or 
inside.Thanks in advance


In the VMD Tk console:

pbc box

If you have problems with VMD, please post to their mailing list.

-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.

Re: [gmx-users] PBC

[mah maz]

I thought so :D
Thanks!

On Thu, Oct 8, 2015 at 9:37 AM, mah maz  wrote:

> Hi Mark
>
> Thank you. I suppose grid can be used without PBC specially when the
> system is in vacuum.
> There are some parameters in the .mdp file that I haven't defined and I
> don't want them to be applied during simulation. However in the mdout.mdp
> They are present eg. gen-seed, emtol, ewald-rtol, Do they play a role
> in the simulation?
>
> Thanks!
>
> On Mon, Oct 5, 2015 at 2:26 PM, mah maz  wrote:
>
>> Hi Mark,
>> Thanks. It seems the default is pbc =xyz. But my question is if I don't
>> use PBC, can I use grid, or grid is only meaningful when PBC is defined?
>>
>> On Mon, Oct 5, 2015 at 11:07 AM, mah maz  wrote:
>>
>>> Dear users,
>>>
>>> If I dont define pbc=no, what is the default type for gromacs? Is it
>>> right if I dont use pbc=no in my system while using grid for ns-type?
>>>
>>> thank you.
>>>
>>
>>
>
-- 
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.

Re: [gmx-users] PBC

[Mark Abraham]

Hi,

On Thu, Oct 8, 2015 at 8:08 AM mah maz  wrote:

> Hi Mark
>
> Thank you. I suppose grid can be used without PBC specially when the system
> is in vacuum.
> There are some parameters in the .mdp file that I haven't defined and I
> don't want them to be applied during simulation. However in the mdout.mdp
> They are present eg. gen-seed, emtol, ewald-rtol, Do they play a role
> in the simulation?
>

Yes, gen-seed kills a kitten and ewald-rtol launches nuclear missiles ;-)
(Stuff that configures inactive algorithms isn't active.)

Mark
-- 
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.

Re: [gmx-users] PBC

[mah maz]

Hi Mark

Thank you. I suppose grid can be used without PBC specially when the system
is in vacuum.
There are some parameters in the .mdp file that I haven't defined and I
don't want them to be applied during simulation. However in the mdout.mdp
They are present eg. gen-seed, emtol, ewald-rtol, Do they play a role
in the simulation?

Thanks!

On Mon, Oct 5, 2015 at 2:26 PM, mah maz  wrote:

> Hi Mark,
> Thanks. It seems the default is pbc =xyz. But my question is if I don't
> use PBC, can I use grid, or grid is only meaningful when PBC is defined?
>
> On Mon, Oct 5, 2015 at 11:07 AM, mah maz  wrote:
>
>> Dear users,
>>
>> If I dont define pbc=no, what is the default type for gromacs? Is it
>> right if I dont use pbc=no in my system while using grid for ns-type?
>>
>> thank you.
>>
>
>
-- 
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.

Re: [gmx-users] PBC

[Mark Abraham]

Hi,

I don't really remember. I suspect not, so I would look up the docs for
ns-type, which should mention limitations, and otherwise try it out. grompp
and/or mdrun are pretty good at complaining about things they can't do.

Mark

On Mon, Oct 5, 2015 at 12:56 PM mah maz  wrote:

> Hi Mark,
> Thanks. It seems the default is pbc =xyz. But my question is if I don't use
> PBC, can I use grid, or grid is only meaningful when PBC is defined?
>
> On Mon, Oct 5, 2015 at 11:07 AM, mah maz  wrote:
>
> > Dear users,
> >
> > If I dont define pbc=no, what is the default type for gromacs? Is it
> right
> > if I dont use pbc=no in my system while using grid for ns-type?
> >
> > thank you.
> >
> --
> 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
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] PBC

[mah maz]

Hi Mark,
Thanks. It seems the default is pbc =xyz. But my question is if I don't use
PBC, can I use grid, or grid is only meaningful when PBC is defined?

On Mon, Oct 5, 2015 at 11:07 AM, mah maz  wrote:

> Dear users,
>
> If I dont define pbc=no, what is the default type for gromacs? Is it right
> if I dont use pbc=no in my system while using grid for ns-type?
>
> thank you.
>
-- 
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.

Re: [gmx-users] PBC

[Mark Abraham]

Hi,

See top of
http://manual.gromacs.org/documentation/5.1/user-guide/mdp-options.html
regarding
defaults. Or you can leave it blank and inspect what gmx grompp writes to
the mdout.mdp. Whether any PBC setting makes sense depends what you're
trying to do, which we don't know.

Mark

On Mon, Oct 5, 2015 at 9:37 AM mah maz  wrote:

> Dear users,
>
> If I dont define pbc=no, what is the default type for gromacs? Is it right
> if I dont use pbc=no in my system while using grid for ns-type?
>
> thank you.
> --
> 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
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] PBC in a closed box.

[André Farias de Moura]

choosing the electrostatic treatment seems to be the least of your
problems: once you turn off the PBC, water molecules will coalesce into a
spherical droplet in order to minimize the surface energy, so you first
have to ask yourself if a nanometric water droplet suits your needs. Not a
simulation issue, rather a surface chemistry fact.

On Tue, Aug 4, 2015 at 2:24 PM, Rodney Versace Babilonia 
rvers...@ccny.cuny.edu wrote:

 Hi all,

 I am trying to simulate the effusion process of water through hole in a
 very thin film. The film is partitioning the water box, I wish to count the
 numbers of waters before and after the simulation in each compartment, but
 I am afraid that the use of periodic boundary conditions will make waters
 from one side going to the other side through the boundaries and that
 affect my counting, in case I turn off the PBC, what kind of electrostatic
 treatment should I use?

 Thanks

 -Rod

 --
 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.




-- 
_

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090
-- 
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.

Re: [gmx-users] PBC issue

[Christopher Neale]

If you just want to make a new, larger water box, try editconf to make the box 
larger and then genbox to add water. Any help beyond than that requires us to 
guess at at least four questions:

What is an unloading simulation
How did you pull a protein
What exactly do you mean by both ends of the protein run out of the boundary 
after pulling
Where should your protein ends connect?

You'll likely get more help if you can be more specific about what you did and 
what the problem is.

CHris.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of tm651209 
tm651...@163.com
Sent: 03 July 2015 06:29
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] PBC issue

Dear all,


I pulled a protein using pdc=xyz, and want to do unloading simulation. The 
problem is both ends of the protein run out of the boundary after pulling. 
After unloading for a while, I found that both ends did not connect to where 
they should connect.
Is there a way that I can regenerate the water box, so that the whole protein 
can stay inside. Therefore, I can use it as a initial state for unloading 
simulation.


Thanks very much.
Regards.
--
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
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] PBC problem in bilayer system

[Justin Lemkul]

On 9/15/14 4:52 AM, shahab shariati wrote:

Dear Tsjerk

Thanks for your reply.

I think that there is another problem, except for visualization.

I obtained the Z coordinate (along the bilayer normal) of the center of
mass of the 4 drug molecules (violet, blue, red and green lines) and
DPPC lipid bilayer (black line) as a function of simulation time, using
g_traj tool.

  The related figure is in following link:



https://www.dropbox.com/s/op8gaxeto4z7qxq/figure.TIF?dl=0

  This Figure is not normal and usual.



Sure it is.  It may just not be the aesthetically pleasing output you want.


  What is your opinion about this issue?



You're asking the same questions that were answered last week:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-September/092153.html

Yes, your plot is normal.  Again, as I said in the linked message, there is no 
side in a periodic system.  You have a continuous water layer.  Your molecules 
simply diffuse around in it.


-Justin

--
==

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

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.

Re: [gmx-users] PBC problem in bilayer system

[Justin Lemkul]

On 9/15/14 12:11 PM, shahab shariati wrote:

Dear Justin

Very very thanks for your time and consideration.

Excuse me for many questions.

I want to make sure my trajectory is valid and accurate for analysis and
then for writing related paper.



It is.


My last question is that can I use this trajectory for doing analysis such
as

g_traj, g_dist, g_density, g_rdf, g_order, g_msd, g_hbond .?



Sure.  Gromacs tools handle PBC effects just fine.  You're getting hung up on 
something that's simply measured crudely.  The absolute z-coordinate in this 
case means very little, precisely for the reasons we've been saying.  The 
difference in z-coordinate between the drug molecules and the bilayer, provided 
that it is measured consistently, is a much more informative metric, assuming 
you're using it to indicate binding events.  The raw output of g_traj in this 
case is not very useful.


-Justin

--
==

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

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.

Re: [gmx-users] PBC problem in bilayer system

[Justin Lemkul]

On 9/15/14 3:12 PM, shahab shariati wrote:

Dear Justin

Thanks for your answer.

You said  The raw output of g_traj in this case is not very useful 

I want to know position and location of drug molecules relative to the DPPC
bilayer during simulation time.

In your opinion, how should I use this tool (g_traj)?



I wouldn't.  You can extract the needed information with a couple of steps of 
post-processing, but it's not worth it when g_dist will do this with no extra 
effort.



Is g_dist appropriate for obtaining distance between center of mass of the
drug molecules and DPPC lipid bilayer as a function of simulation time?



Yes, use g_dist.  But the x- and y- components aren't useful, so the (absolute 
value of) the z-component of the distance is what you need.


-Justin

--
==

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

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.

Re: [gmx-users] PBC problem in bilayer system

[Justin Lemkul]

On 9/13/14 7:59 AM, shahab shariati wrote:

Dear Justin

you said  The -trans option takes a vector where you specify the amount of
translation to apply 

I do not know what vector should be considered in -trans option.



Well, what have you tried?  You need to shift your system along z, the direction 
doesn't really matter.  The exact magnitude depends on the dimensions of the system.


-Justin

--
==

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

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.

Re: [gmx-users] PBC problem in bilayer system

[Justin Lemkul]

On 9/14/14 8:43 AM, shahab shariati wrote:

Dear Justin

Thanks for your reply.

I inserted 4 drug molecules in close vicinity to the membrane surface
in water phase, in one side of bilayer (for example, top). In the
different frames of trajectory, some of drug molecules (one or two
drug molecules) are seen in other side of bilayer (bottom).  I really
do not know what thing has to be translated. Should I shift all
components of my system (DPPC, drug, and water molecules) along z or
only drug molecules?



Translate the whole system.




The dimensions of my system in final gro file are as follows:

  6.46063   6.57889   8.30034



Based on your reply (The exact magnitude depends on the dimensions of the
system), should I use following command:



trjconv –trans 6.46063   6.57889   8.30034



If you used pressure coupling, no, because the box dimensions will change over 
time.  Moreover, you do not want to change x and y.  As I said before, you want 
to translate along z.  Try a few values and see if you get a reasonable result.


-Justin

--
==

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

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.

Re: [gmx-users] PBC problem in bilayer system

[Justin Lemkul]

On 9/14/14 8:58 AM, shahab shariati wrote:

Dear Justin




I did MD simulation on the NPT ensemble:


pcoupl  =  Berendsen

pcoupltype  =  semiisotropic

ref_p =  1.0



In this condition, to solve this problem, what should I do?



I have already said a few times what to do.  Try running trjconv and see what 
you get rather than waiting for email responses.  You'll accomplish more.


-Justin

--
==

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

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.

Re: [gmx-users] PBC problem in bilayer system

[Justin Lemkul]

On 9/14/14 9:52 AM, shahab shariati wrote:

Dear Justin


I did following:


trjconv -f *.xtc -s *.tpr -n *.ndx -o **.xtc -trans 6.46063 6.57889 9

Based on your reply*, *I translated all system along the z.

I used x and y according to box dimension.

I used 9, instead of z dimension (8.30034), for z.

When I see **.xtc using vmd, problem was not solved.

Should I increase or decrease z value for -trans option?



Start by following what I've told you:

1. Do not change x and y; set them to zero in -trans
2. A value of 9 for z makes no sense if your box is not that large; try 8 or 
less
3. Use -pbc mol when translating

-Justin

--
==

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

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.

Re: [gmx-users] PBC problem in bilayer system

[Justin Lemkul]

On 9/14/14 10:29 AM, shahab shariati wrote:

Dear Justin

Based on your previous reply, I used following:

trjconv -f *.xtc -s *.tpr -n *.ndx -o **.xtc  -pbc mol –trans 0 0 7


When I see **.xtc using vmd, unfortunately, problem was not solved.


Please see the following link:

https://www.dropbox.com/s/345o7lvc9z4jwln/figure%204.TIF?dl=0



From that picture, it is clear that it is simply impossible to gather all of 
the drug molecules on one side of the membrane.  They have bound to both sides; 
there's no changing that since it's not an imaging issue.  If some were bound 
and others were simultaneously still free in the water layer, it could be done. 
 In this case, it cannot.


-Justin

--
==

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

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.

Re: [gmx-users] PBC problem in bilayer system

[Tsjerk Wassenaar]

Hi,

Just a small side note. There's nothing intrinsically nonsensical about
translating more than a box size. The PBC are translation invariant, so you
can do anything and have the system be fine. However, for visualization,
translating one box length, and put the stuff back in the box, makes as
much sense as doing nothing at all.

Cheers,

Tsjerk
On Sep 14, 2014 3:55 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 9/14/14 9:52 AM, shahab shariati wrote:

 Dear Justin


 I did following:


 trjconv -f *.xtc -s *.tpr -n *.ndx -o **.xtc -trans 6.46063 6.57889 9

 Based on your reply*, *I translated all system along the z.

 I used x and y according to box dimension.

 I used 9, instead of z dimension (8.30034), for z.

 When I see **.xtc using vmd, problem was not solved.

 Should I increase or decrease z value for -trans option?


 Start by following what I've told you:

 1. Do not change x and y; set them to zero in -trans
 2. A value of 9 for z makes no sense if your box is not that large; try 8
 or less
 3. Use -pbc mol when translating

 -Justin

 --
 ==

 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

 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
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] PBC problem in bilayer system

[Justin Lemkul]

On 9/11/14 8:01 AM, shahab shariati wrote:

Dear gromacs users

When I see trajectory file using vmd, there is state showed in following link:

https://www.dropbox.com/s/g8i934atodrb7te/figure2.TIF?dl=0

in initial structure, all 4 drugs were  inserted in water phase, in one side of
bilayer.

Is this state normal?



Yes, because there's no such thing as a side in a periodic system.  You have a 
water layer that is continuous in z, so the molecules are free to diffuse around 
as they please.  It may not be possible to re-image the trajectory such that all 
of the drug molecules are positioned in the same region in the unit cell.  You 
can try the translation options of trjconv (in conjunction with -pbc mol) to try 
to shift the system up or down to get everything to fit, but then of course the 
lipids can jump around.  Perhaps additional calls to trjconv can account for 
that (i.e. another round of -pbc nojump after translating).


-Justin

--
==

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

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.

Re: [gmx-users] PBC problem in bilayer system

[Michael Carter]

Hi,

Try -pbc nojump

Best,
Mike

On 09/09/2014 15:11, shahab shariati shahab.shari...@gmail.com wrote:

Dear gromacs users

I did MD simulation of my system containing DPPC lipids + water molecule
and 4 drug molecules.

I saw trajectory file using VMD.

Unfortunately, drug molecules jump across the box.

How to resolve this PBC problem?

which of -pbc options (none, mol, res, atom, nojump, cluster or whole) in
trjconv tool is appropriate for my case?


Any help will highly appreciated.
-- 
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.

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the 
message is received by anyone other than the addressee, please return the 
message to the sender by replying to it and then delete the message from your 
computer and network.
-- 
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.

Re: [gmx-users] PBC problem in bilayer system

[Michael Carter]

Also if you want to fix the position on the centre of mass (no rotating or
translating) try

-pbc nojump

Followed by -fit rot+trans

Remember to use you new .xtc from your no jump command for the -fit
command. Then view in vmd and your molecules will not jump, rotate, or
translate around the box.

Mike

On 09/09/2014 15:12, Michael Carter michael.car...@icr.ac.uk wrote:

Hi,

Try -pbc nojump

Best,
Mike

On 09/09/2014 15:11, shahab shariati shahab.shari...@gmail.com wrote:

Dear gromacs users

I did MD simulation of my system containing DPPC lipids + water molecule
and 4 drug molecules.

I saw trajectory file using VMD.

Unfortunately, drug molecules jump across the box.

How to resolve this PBC problem?

which of -pbc options (none, mol, res, atom, nojump, cluster or whole) in
trjconv tool is appropriate for my case?


Any help will highly appreciated.
-- 
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.

The Institute of Cancer Research: Royal Cancer Hospital, a charitable
Company Limited by Guarantee, Registered in England under Company No.
534147 with its Registered Office at 123 Old Brompton Road, London SW7
3RP.

This e-mail message is confidential and for use by the addressee only.
If the message is received by anyone other than the addressee, please
return the message to the sender by replying to it and then delete the
message from your computer and network.
-- 
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.

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the 
message is received by anyone other than the addressee, please return the 
message to the sender by replying to it and then delete the message from your 
computer and network.
-- 
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.

Re: [gmx-users] PBC problems??

[Justin Lemkul]

On 5/23/14, 2:51 PM, Steve Seibold wrote:

My protein breaks according to viewing the traj in VMD and graphing the RMSD of 
the protein C-terminus


I have tried all combinations of trjconv -pbc -center
-box center and nothing works..I was able to get online and find a
tutorial that says trjconv -pbc mol, should stop the problem, but this
failedIsn't there a way for the protein and water to be wrapped or COM
calculations done DURING MD to remove translation, rotation so that post-MD
modification of trajectories is unnecessary??...If I make an index group of the


The integration doesn't need to follow our visualization convenience, so there's 
no reason to sacrifice performance to re-wrap coordinates on the fly.



N-terminus of the protein this problems goes away or if I use the whole
protein...It is only when I attempt to get the rms of the C-terminus region
that I get this graphing problem (traj plots look like Histograms)Not sure 
what this means since if I observe
the trajectories in VMD the whole protein breaks up


Centering a single protein within a box should be very easy using any of the 
options you have posted.  trjconv -pbc mol -ur compact -center should be all 
that's necessary for a simple system like this.  Are you sure the box is large 
enough to accommodate the protein?  If it keeps breaking in spite of trjconv, 
that might suggest your box is not suitable, such that re-imaging can't fix things.


-Justin

--
==

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

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.

Re: [gmx-users] PBC correction to visualize a protein-membrane structure

[Juan Munoz-Garcia]

Dear Justin,

you’re right. The problem was the system was not center properly in the initial 
.gro file. Now it works.

Thank you very much.

Juan C.

On 5/17/14, 5:49 AM, Juan Munoz-Garcia wrote:
 Dear Mark,

 I’ve used numbers. Just indicated them as x_box/2, etc to be clearer.


There are two possibilities:

1. You built the system wrong and trjconv can't fix it.  Without the full
sequence of commands used to build the system, no one can provide any advice
here.  Providing an image that shows the unit cell (pbc box in the Tcl window
in VMD) can also be informative in this regard.

2. This is a PBC issue that should be resolvable, probably within a few
iterations of trjconv.  See
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow.
  Often times, it helps to start with a new .tpr file that has the system
centered properly when remove jumps, etc.


-- 
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.

Re: [gmx-users] PBC correction to visualize a protein-membrane structure

[Justin Lemkul]

On 5/16/14, 4:04 AM, Juan Munoz-Garcia wrote:

Dear GROMACS users,

I’m preparing a protein-membrane structure to use as input for MD. I’ve just
carried out a short minimisation of the lipids applying restraints to the
protein, after which I’ve obtained the attached structure. I’ve tried all
types of trjconv combinations with -pbc -ur or -fit, but it doesn’t work, I
still get the same structure. Even more weird is that when I turn on the
periodic images option in vmd I still don’t see the right protein embedded
into the lipid bilayer. As this can’t be a real effect of minimisation, I'd
like to ask for your advice.



The mailing list does not accept attachments.  Please post links to images or 
files to download.  An exact sequence of commands would be useful, as well.


-Justin

--
==

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

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.

Re: [gmx-users] PBC correction to visualize a protein-membrane structure

[Juan Munoz-Garcia]

Thank you Justin,

please find a dropbox link to the image below.

I’ve used

trjconv_mpi -f NPT.trr -o NPT_2.trr -s NPT.tpr -pbc whole
trjconv_mpi -f NPT_2.trr -o NPT_PBC.trr -s NPT.tpr -pbc mol -ur compact -center

and different combinations of those

https://www.dropbox.com/s/az1gvb299y6wh8h/Screen%20Shot%202014-05-06%20at%2021.15.07.png

Thank you.
Regards.
Juan C.

-- 
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.

Re: [gmx-users] PBC correction to visualize a protein-membrane structure

[Justin Lemkul]

On 5/16/14, 9:08 AM, Juan Munoz-Garcia wrote:

Thank you Justin,

please find a dropbox link to the image below.

I’ve used

trjconv_mpi -f NPT.trr -o NPT_2.trr -s NPT.tpr -pbc whole
trjconv_mpi -f NPT_2.trr -o NPT_PBC.trr -s NPT.tpr -pbc mol -ur compact -center

and different combinations of those

https://www.dropbox.com/s/az1gvb299y6wh8h/Screen%20Shot%202014-05-06%20at%2021.15.07.png



Your system was probably centered at z=0 instead of z = z_box/2 (commands used 
for building the system would also help - I guess I should have been more 
clear), hence it's getting split across PBC.  trjconv -trans in conjunction with 
-pbc mol should be what you need.


-Justin

--
==

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

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.

Re: [gmx-users] PBC correction to visualize a protein-membrane structure

[Juan Munoz-Garcia]

Dear Justin,

thank you. I’ve tried the following but neither of them worked, I get the same 
result.

trjconv -f input.gro -o output.gro -s .tpr -trans 0 0  z_box/2 -pbc mol -ur 
compact

trjconv -f input.gro -o output.gro -s tpr -trans x_box/2  y_box/2  z_box/2 -pbc 
mol -ur compact


This is the last line of my input.gro file

19.51671  19.51671  13.80040   0.0   0.0   0.0   0.0   9.75836  
 9.75836

Juan C.


Your system was probably centered at z=0 instead of z = z_box/2 (commands used
for building the system would also help - I guess I should have been more
clear), hence it's getting split across PBC.  trjconv -trans in conjunction with
-pbc mol should be what you need.

-Justin

--

Begin forwarded message:

From: Juan Carlos Munoz Garcia 
juan.munoz-gar...@bioch.ox.ac.ukmailto:juan.munoz-gar...@bioch.ox.ac.uk
Subject: Re: PBC correction to visualize a protein-membrane structure
Date: 16 May 2014 14:08:50 BST
To: 
gromacs.org_gmx-users@maillist.sys.kth.semailto:gromacs.org_gmx-users@maillist.sys.kth.se

Thank you Justin,

please find a dropbox link to the image below.

I’ve used

trjconv_mpi -f NPT.trr -o NPT_2.trr -s NPT.tpr -pbc whole
trjconv_mpi -f NPT_2.trr -o NPT_PBC.trr -s NPT.tpr -pbc mol -ur compact -center

and different combinations of those

https://www.dropbox.com/s/az1gvb299y6wh8h/Screen%20Shot%202014-05-06%20at%2021.15.07.png

Thank you.
Regards.
Juan C.


-- 
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.

Re: [gmx-users] PBC correction to visualize a protein-membrane structure

[Mark Abraham]

On May 16, 2014 7:03 PM, Juan Munoz-Garcia 
juan.munoz-gar...@bioch.ox.ac.uk wrote:

 Dear Justin,

 thank you. I’ve tried the following but neither of them worked, I get the
same result.

 trjconv -f input.gro -o output.gro -s .tpr -trans 0 0  z_box/2 -pbc mol
-ur compact

 trjconv -f input.gro -o output.gro -s tpr -trans x_box/2  y_box/2
 z_box/2 -pbc mol -ur compact

You need to use numbers.

Mark


 This is the last line of my input.gro file

 19.51671  19.51671  13.80040   0.0   0.0   0.0   0.0
9.75836   9.75836

 Juan C.


 Your system was probably centered at z=0 instead of z = z_box/2 (commands
used
 for building the system would also help - I guess I should have been more
 clear), hence it's getting split across PBC.  trjconv -trans in
conjunction with
 -pbc mol should be what you need.

 -Justin

 --

 Begin forwarded message:

 From: Juan Carlos Munoz Garcia juan.munoz-gar...@bioch.ox.ac.ukmailto:
juan.munoz-gar...@bioch.ox.ac.uk
 Subject: Re: PBC correction to visualize a protein-membrane structure
 Date: 16 May 2014 14:08:50 BST
 To: gromacs.org_gmx-users@maillist.sys.kth.semailto:
gromacs.org_gmx-users@maillist.sys.kth.se

 Thank you Justin,

 please find a dropbox link to the image below.

 I’ve used

 trjconv_mpi -f NPT.trr -o NPT_2.trr -s NPT.tpr -pbc whole
 trjconv_mpi -f NPT_2.trr -o NPT_PBC.trr -s NPT.tpr -pbc mol -ur compact
-center

 and different combinations of those


https://www.dropbox.com/s/az1gvb299y6wh8h/Screen%20Shot%202014-05-06%20at%2021.15.07.png

 Thank you.
 Regards.
 Juan C.


 --
 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
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pbc problems

[申昊]

  Hello everyone!
 
  I am a new one of gromacs. When a simulation of protein in water is 
  finished,
  should i first use the command of trjconv to remove pbc conditions(with
  nojump or mol), and then began analyze the new trajectory(rmsd, Rg and some
  other parameters)? Is the result believable without removing the pbc
  conditions or it is necessary for some specific calculations?
 
 
 Most Gromacs programs deal with PBC with no manipulation required, some do 
 not. 
   g_rms needs a properly processed trajectory.
 
 -Justin
 

Thank you for your response! 
As you said, i also found the Rmsd by using -nojump or -mol is different from 
that without these commands. And i can not 
decide which one is more accurate. Furthermore, can you list some other 
parameters that need removed pbc conditions? 
such as SDF calculation ... 


-- 
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.

Re: [gmx-users] PBC problem after MD

[Mark Abraham]

If there's a problem, trjconv can handle it with the use of the right index
groups, as suggested at
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions.
But it can't keep these three things together if there's no index group
that describes these three things. You may need to generate it with
make_ndx.

Mark


On Thu, Feb 13, 2014 at 11:36 AM, SEMRAN İPEK semrani...@gmail.com wrote:

 Hi all,

 I am aware of that this topic has been discussed for many times. However, I
 need your more guidance  whether I am experiencing PBC problem after MD or
 not.
 My MD box has enzyme+ligand+coenzyme complex. As I have already wrote to
 the user list, I am using the force field parameters from literature for
 the ligand. And other paramaters related to MD has been checked twice.
 After MD what I have seen is that ligand is getting far away from the
 active site of the coenzyme.
 Justin has mentioned that this is the PBC problem (thank you Justin for
 your endless and comprehensive support.). Whatever I do was useless to cure
 the PBC problem.
 Could you please check my distance file showing the distance between ligand
 and coenzyme during MD simulation?
 And could you please share your experince if this is the PBC problem or
 not?if yes, why trjconvc can not handle it?


 Best Regards,

 --ipek

 --
 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
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] PBC problem after MD

[ipek]

Dear Kannan,


Thank you for your fast response. The problem is that the ligand is as far
as 16 Ang., which is too far away from the coenzyme for any kind of bonding.
here is the link for downloading my dist.jpeg file.http://we.tl/ACencjievC

Do you think that this is a real PBC problem?

Really looking forward to hearing from you.


Best,

ipek

--
View this message in context: 
http://gromacs.5086.x6.nabble.com/PBC-problem-after-MD-tp5014519p5014522.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
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.

Re: [gmx-users] pbc problem

[Justin Lemkul]

On 2/2/14, 7:15 AM, Atila Petrosian wrote:

Dear Justin and Tsjerk

you said  Some tools handle PBC properly, some don't .

I want to know exactly which tools of gromacs handle PBC properly.

Can I find these tools in manual?



No, because it's not possible to test every single command that the user might 
issue and keep a reliable database of such information.



I did simulation of a system containing protein and cnt using gromacs 4.5.6.

When I see trajectory by VMD, in some frames, protein atoms exit one side
of box
and enter opposite side of box. I want to do analysis of trajectory. I do
not know
exactly this state is pbc problem or not.



Again, that depends entirely upon the command you're using.  Tools like g_rms 
have problems when molecules are split across PBC.  Other tools like g_dist or 
g_msd handle the situation better.  If the protein is the only problematic 
molecule, it should be rather trivial to fix the PBC issues with trjconv 
-center, trjconv -pbc nojump, trjconv -pbc mol -ur compact, or trjconv -fit 
translation, or perhaps some sequence of those.  Please refer to the PBC link I 
have posted several times this week.


-Justin

--
==

Justin A. Lemkul, Ph.D.
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

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.

Re: [gmx-users] pbc

[kannan]

Thank you for your reply Tsjerk..
I do many Trjconv -pbc mol -ur compact -center. but it doesn't help..

this is PBC. if i center protein the ligand goes other side at end of
simulation. if i center ligand, then protein goes... if i center both, its
trajectory is same as old one.

How to overcome this problem? Please give some suggestion.

or shall i analyse without trjconv -pbc with raw trajector?

Thank you
best regards,
kannan s


On Fri, Jan 31, 2014 at 5:03 PM, Tsjerk Wassenaar [via GROMACS] 
ml-node+s5086n501418...@n6.nabble.com wrote:

 Hi Kannan,

 Depends a bit. Some tools handle PBC properly, some don't.

 Cheers,

 Tsjerk


 On Fri, Jan 31, 2014 at 9:30 AM, Kannan S [hidden 
 email]http://user/SendEmail.jtp?type=nodenode=5014189i=0
 wrote:

  Is there any problem when we analyse the protein-ligand complex
 simulation
  withPBC problem without using -trjconv?
 
  Thank you
  kannan s
  --
  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 [hidden 
  email]http://user/SendEmail.jtp?type=nodenode=5014189i=1.

 



 --
 Tsjerk A. Wassenaar, Ph.D.
 --
 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 [hidden 
 email]http://user/SendEmail.jtp?type=nodenode=5014189i=2.



 --
  If you reply to this email, your message will be added to the discussion
 below:
 http://gromacs.5086.x6.nabble.com/pbc-tp5014184p5014189.html
  To start a new topic under GROMACS Users Forum, email
 ml-node+s5086n4370410...@n6.nabble.com
 To unsubscribe from GROMACS, click 
 herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=4385198code=a2FubmFuLjI5MTBAZ21haWwuY29tfDQzODUxOTh8NjA3OTM5OTMw
 .
 NAMLhttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml



--
View this message in context: 
http://gromacs.5086.x6.nabble.com/pbc-tp5014184p5014191.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
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.

Re: [gmx-users] pbc

[Justin Lemkul]

On 1/31/14, 7:09 AM, kannan wrote:

Thank you for your reply Tsjerk..
I do many Trjconv -pbc mol -ur compact -center. but it doesn't help..

this is PBC. if i center protein the ligand goes other side at end of
simulation. if i center ligand, then protein goes... if i center both, its
trajectory is same as old one.

How to overcome this problem? Please give some suggestion.

or shall i analyse without trjconv -pbc with raw trajector?



As Tsjerk said, some tools handle PBC well, some don't.  If you're having a 
specific issue with a specific tool, then you will need to account for 
periodicity effects.  If not, then there is no need to worry.  With 
protein-ligand systems and other complexes, -pbc nojump is usually the best 
first step.  See 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow.


-Justin

--
==

Justin A. Lemkul, Ph.D.
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

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.

Re: [gmx-users] pbc

[kannan]

Thank you very much for your valuable suggestion Justin...

best regards,
kannan s

I


On Fri, Jan 31, 2014 at 6:31 PM, Justin Lemkul [via GROMACS] 
ml-node+s5086n5014192...@n6.nabble.com wrote:



 On 1/31/14, 7:09 AM, kannan wrote:

  Thank you for your reply Tsjerk..
  I do many Trjconv -pbc mol -ur compact -center. but it doesn't help..
 
  this is PBC. if i center protein the ligand goes other side at end of
  simulation. if i center ligand, then protein goes... if i center both,
 its
  trajectory is same as old one.
 
  How to overcome this problem? Please give some suggestion.
 
  or shall i analyse without trjconv -pbc with raw trajector?
 

 As Tsjerk said, some tools handle PBC well, some don't.  If you're having
 a
 specific issue with a specific tool, then you will need to account for
 periodicity effects.  If not, then there is no need to worry.  With
 protein-ligand systems and other complexes, -pbc nojump is usually the
 best
 first step.  See

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


 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 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

 [hidden email] http://user/SendEmail.jtp?type=nodenode=5014192i=0 |
 (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 [hidden 
 email]http://user/SendEmail.jtp?type=nodenode=5014192i=1.



 --
  If you reply to this email, your message will be added to the discussion
 below:
 http://gromacs.5086.x6.nabble.com/pbc-tp5014184p5014192.html
  To start a new topic under GROMACS Users Forum, email
 ml-node+s5086n4370410...@n6.nabble.com
 To unsubscribe from GROMACS, click 
 herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=4385198code=a2FubmFuLjI5MTBAZ21haWwuY29tfDQzODUxOTh8NjA3OTM5OTMw
 .
 NAMLhttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml



--
View this message in context: 
http://gromacs.5086.x6.nabble.com/pbc-tp5014184p5014210.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
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.

Re: [gmx-users] pbc problem

[tarak karmakar]

Hi,
trjconv -s topol.tpr -f traj -pbc mol -o traj_modified

select '0' for the entire system

You can try using either 'mol' or 'nojump' depending on your visualization
needs.

cheers,
Tarak


On Wed, Jan 29, 2014 at 3:39 PM, Atila Petrosian
atila.petros...@gmail.comwrote:

 Dear Gromacs users

 I did simulation of a system containing protein and cnt using gromacs
 4.5.6.

 When I see trajectory by VMD, in some frames, protein atoms exit one side
 of box
 and enter opposite side of box (pbc problem). I know I should use -pbc
 option of
 trjconv tool. But I do not know exactly which of none, mol, res, atom,
 nojump,
 cluster or whole is appropriate for me. The below link shows one frame of
 trajectory:

 https://www.dropbox.com/s/vur8fh1apvp79lm/pbc%20problem.bmp

 Any help will highly appreciated
 --
 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
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pbc problem

[Justin Lemkul]

On 1/29/14, 9:13 AM, Atila Petrosian wrote:

Dear Justin

Thanks for your reply.

To obtain modified trajectory and then comparing with original trajectory,
I do not know exactly which of none, mol, res, atom, nojump, cluster or
whole is appropriate for me.



In a simple case like this, many of the options may produce equivalent outcomes. 
 Explore the list archive a bit, because periodicity is discussed frequently. 
Also consult 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow 
and play around with trjconv - nothing supplants a bit of trial and error 
sometimes, especially with a Swiss army knife program like trjconv.


-Justin

--
==

Justin A. Lemkul, Ph.D.
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

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.