Re: [gmx-users] regarding pbc issue

[Justin Lemkul]

On 1/17/18 12:06 PM, Rose wrote:

Thank you so much,I've got it now.

we know that for example 2 molecule can not stick to each other they just close 
enough till repulse  each other.
Now, imagine pulling, if I can not see "really broken" structures in classicalMD , so 
what would be my criterion and clue to say that:"that's enough, you shouldn't pull it 
MORE?"

Totally, how can i know the Max pulling ?

I have PMF schemes which show repulsion( after interaction distance the 
potential get less minus and tend to get more positive but they just stop in 
0kJ and not any positive potential. It happened for every AA which i pull it 
through sheet, so i doubt to my results.


A PMF of zero means the biased groups are (effectively) no longer 
interacting. You should expect this.


This thread is well off topic of the original post; if you have further 
questions, start a new thread to avoid hijacking this one and 
complicating the archive further.


-Justin


Sorry for poor english

With regards
Sent from my iPhone


On Jan 17, 2018, at 19:57, Justin Lemkul  wrote:




On 1/17/18 11:23 AM, Rose wrote:
I mean, sometimes structures may really break or collapse, in these situations 
trjconv won't show these broken structures whole yes?
just will show them broken (as they really are) yes?

In the context of the question I was answering, "broken" means that it appears bonds have broken 
and molecules appear at either side of a periodic boundary. That instance is always fixed by proper use of 
trjconv. Bonds can't break or form during classical MD, so if trjconv leaves "broken" molecules 
behind, then you've got a topology issue. But I'd wager that about 99.999% of the cases that involve 
"broken" molecules are normal PBC issues and nothing more.

But, to answer your question, no, trjconv won't fix a situation in which the 
user has supplied an incorrect topology.

-Justin


Sent from my iPhone


On Jan 17, 2018, at 18:15, Justin Lemkul  wrote:




On 1/17/18 9:40 AM, Rose wrote:
You mean if -pbc could make molecule whole,everything is ok, but if not it 
means the molecule was broken from first, yes?

mdrun writes "broken" coordinates because the physics does not depend on our 
visualization convenience. Most programs account for PBC. Some don't. It is generally a 
safe practice to just make molecules whole as your first step in trjconv and avoid any 
ambiguity.

-Justin


Sent from my iPhone


On Jan 17, 2018, at 16:19, Justin Lemkul  wrote:




On 1/17/18 5:51 AM, Vidya R wrote:
Hi Justin,

I got the same result as you said.

What confused me was,  when I viewed movie.pdb file generated by the
following command,

  gmx trjconv -pbc nojump -s PRD-SMP3.gro -f PRD-SMP3.xtc -e 1.0 -n
index.ndx -o movie.pdb


two hydrogen molecules of my organic compound, were unbonded to my molecule
(which is not supposed to be).  They are far away from molecules (their
bonds were broken)

Is it a pbc problem?

Because, when I used

gmx trjconv -pbc whole -s PRD.tpr -f PRD.xtc -o trajwhole.xtc
gmx trjconv -pbc nojump -s PRD.tpr -f trajwhole.xtc -o trajcluster.xtc
gmx trjconv -pbc mol -center -s PRD.tpr -f trajcluster.xtc -o newtraj.xtc


and created a .pdb file with newtraj.xtc, the whole molecule was intact.

Making molecules whole should always be the first step. If you try to remove jumps with 
"broken" molecules, what you visualize will be garbage. A separate issue is 
with respect to the analysis programs - many are PBC-aware and can handle the original 
trajectory without manipulation.

-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

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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

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Re: [gmx-users] regarding pbc issue

[Rose]

Thank you so much,I've got it now.

we know that for example 2 molecule can not stick to each other they just close 
enough till repulse  each other.
Now, imagine pulling, if I can not see "really broken" structures in 
classicalMD , so what would be my criterion and clue to say that:"that's 
enough, you shouldn't pull it MORE?"

Totally, how can i know the Max pulling ?

I have PMF schemes which show repulsion( after interaction distance the 
potential get less minus and tend to get more positive but they just stop in 
0kJ and not any positive potential. It happened for every AA which i pull it 
through sheet, so i doubt to my results.

Sorry for poor english

With regards
Sent from my iPhone

> On Jan 17, 2018, at 19:57, Justin Lemkul  wrote:
> 
> 
> 
>> On 1/17/18 11:23 AM, Rose wrote:
>> I mean, sometimes structures may really break or collapse, in these 
>> situations trjconv won't show these broken structures whole yes?
>> just will show them broken (as they really are) yes?
> 
> In the context of the question I was answering, "broken" means that it 
> appears bonds have broken and molecules appear at either side of a periodic 
> boundary. That instance is always fixed by proper use of trjconv. Bonds can't 
> break or form during classical MD, so if trjconv leaves "broken" molecules 
> behind, then you've got a topology issue. But I'd wager that about 99.999% of 
> the cases that involve "broken" molecules are normal PBC issues and nothing 
> more.
> 
> But, to answer your question, no, trjconv won't fix a situation in which the 
> user has supplied an incorrect topology.
> 
> -Justin
> 
>> Sent from my iPhone
>> 
>>> On Jan 17, 2018, at 18:15, Justin Lemkul  wrote:
>>> 
>>> 
>>> 
 On 1/17/18 9:40 AM, Rose wrote:
 You mean if -pbc could make molecule whole,everything is ok, but if not it 
 means the molecule was broken from first, yes?
>>> mdrun writes "broken" coordinates because the physics does not depend on 
>>> our visualization convenience. Most programs account for PBC. Some don't. 
>>> It is generally a safe practice to just make molecules whole as your first 
>>> step in trjconv and avoid any ambiguity.
>>> 
>>> -Justin
>>> 
 Sent from my iPhone
 
> On Jan 17, 2018, at 16:19, Justin Lemkul  wrote:
> 
> 
> 
>> On 1/17/18 5:51 AM, Vidya R wrote:
>> Hi Justin,
>> 
>> I got the same result as you said.
>> 
>> What confused me was,  when I viewed movie.pdb file generated by the
>> following command,
>> 
>>  gmx trjconv -pbc nojump -s PRD-SMP3.gro -f PRD-SMP3.xtc -e 1.0 -n
>> index.ndx -o movie.pdb
>> 
>> 
>> two hydrogen molecules of my organic compound, were unbonded to my 
>> molecule
>> (which is not supposed to be).  They are far away from molecules (their
>> bonds were broken)
>> 
>> Is it a pbc problem?
>> 
>> Because, when I used
>> 
>> gmx trjconv -pbc whole -s PRD.tpr -f PRD.xtc -o trajwhole.xtc
>> gmx trjconv -pbc nojump -s PRD.tpr -f trajwhole.xtc -o trajcluster.xtc
>> gmx trjconv -pbc mol -center -s PRD.tpr -f trajcluster.xtc -o newtraj.xtc
>> 
>> 
>> and created a .pdb file with newtraj.xtc, the whole molecule was intact.
> Making molecules whole should always be the first step. If you try to 
> remove jumps with "broken" molecules, what you visualize will be garbage. 
> A separate issue is with respect to the analysis programs - many are 
> PBC-aware and can handle the original trajectory without manipulation.
> 
> -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
> 
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> send a mail to gmx-users-requ...@gromacs.org.
>>> -- 
>>> ==
>>> 
>>> 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 

Re: [gmx-users] regarding pbc issue

[Justin Lemkul]

On 1/17/18 11:23 AM, Rose wrote:

I mean, sometimes structures may really break or collapse, in these situations 
trjconv won't show these broken structures whole yes?
just will show them broken (as they really are) yes?


In the context of the question I was answering, "broken" means that it 
appears bonds have broken and molecules appear at either side of a 
periodic boundary. That instance is always fixed by proper use of 
trjconv. Bonds can't break or form during classical MD, so if trjconv 
leaves "broken" molecules behind, then you've got a topology issue. But 
I'd wager that about 99.999% of the cases that involve "broken" 
molecules are normal PBC issues and nothing more.


But, to answer your question, no, trjconv won't fix a situation in which 
the user has supplied an incorrect topology.


-Justin


Sent from my iPhone


On Jan 17, 2018, at 18:15, Justin Lemkul  wrote:




On 1/17/18 9:40 AM, Rose wrote:
You mean if -pbc could make molecule whole,everything is ok, but if not it 
means the molecule was broken from first, yes?

mdrun writes "broken" coordinates because the physics does not depend on our 
visualization convenience. Most programs account for PBC. Some don't. It is generally a 
safe practice to just make molecules whole as your first step in trjconv and avoid any 
ambiguity.

-Justin


Sent from my iPhone


On Jan 17, 2018, at 16:19, Justin Lemkul  wrote:




On 1/17/18 5:51 AM, Vidya R wrote:
Hi Justin,

I got the same result as you said.

What confused me was,  when I viewed movie.pdb file generated by the
following command,

  gmx trjconv -pbc nojump -s PRD-SMP3.gro -f PRD-SMP3.xtc -e 1.0 -n
index.ndx -o movie.pdb


two hydrogen molecules of my organic compound, were unbonded to my molecule
(which is not supposed to be).  They are far away from molecules (their
bonds were broken)

Is it a pbc problem?

Because, when I used

gmx trjconv -pbc whole -s PRD.tpr -f PRD.xtc -o trajwhole.xtc
gmx trjconv -pbc nojump -s PRD.tpr -f trajwhole.xtc -o trajcluster.xtc
gmx trjconv -pbc mol -center -s PRD.tpr -f trajcluster.xtc -o newtraj.xtc


and created a .pdb file with newtraj.xtc, the whole molecule was intact.

Making molecules whole should always be the first step. If you try to remove jumps with 
"broken" molecules, what you visualize will be garbage. A separate issue is 
with respect to the analysis programs - many are PBC-aware and can handle the original 
trajectory without manipulation.

-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

==

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--
==

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

==

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--
==

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

==

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Re: [gmx-users] regarding pbc issue

[Rose]

I mean, sometimes structures may really break or collapse, in these situations 
trjconv won't show these broken structures whole yes?
just will show them broken (as they really are) yes?

Sent from my iPhone

> On Jan 17, 2018, at 18:15, Justin Lemkul  wrote:
> 
> 
> 
>> On 1/17/18 9:40 AM, Rose wrote:
>> You mean if -pbc could make molecule whole,everything is ok, but if not it 
>> means the molecule was broken from first, yes?
> 
> mdrun writes "broken" coordinates because the physics does not depend on our 
> visualization convenience. Most programs account for PBC. Some don't. It is 
> generally a safe practice to just make molecules whole as your first step in 
> trjconv and avoid any ambiguity.
> 
> -Justin
> 
>> Sent from my iPhone
>> 
>>> On Jan 17, 2018, at 16:19, Justin Lemkul  wrote:
>>> 
>>> 
>>> 
 On 1/17/18 5:51 AM, Vidya R wrote:
 Hi Justin,
 
 I got the same result as you said.
 
 What confused me was,  when I viewed movie.pdb file generated by the
 following command,
 
  gmx trjconv -pbc nojump -s PRD-SMP3.gro -f PRD-SMP3.xtc -e 1.0 -n
 index.ndx -o movie.pdb
 
 
 two hydrogen molecules of my organic compound, were unbonded to my molecule
 (which is not supposed to be).  They are far away from molecules (their
 bonds were broken)
 
 Is it a pbc problem?
 
 Because, when I used
 
 gmx trjconv -pbc whole -s PRD.tpr -f PRD.xtc -o trajwhole.xtc
 gmx trjconv -pbc nojump -s PRD.tpr -f trajwhole.xtc -o trajcluster.xtc
 gmx trjconv -pbc mol -center -s PRD.tpr -f trajcluster.xtc -o newtraj.xtc
 
 
 and created a .pdb file with newtraj.xtc, the whole molecule was intact.
>>> Making molecules whole should always be the first step. If you try to 
>>> remove jumps with "broken" molecules, what you visualize will be garbage. A 
>>> separate issue is with respect to the analysis programs - many are 
>>> PBC-aware and can handle the original trajectory without manipulation.
>>> 
>>> -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.
> 
> -- 
> ==
> 
> 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
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Re: [gmx-users] regarding pbc issue

[Justin Lemkul]

On 1/17/18 9:40 AM, Rose wrote:

You mean if -pbc could make molecule whole,everything is ok, but if not it 
means the molecule was broken from first, yes?


mdrun writes "broken" coordinates because the physics does not depend on 
our visualization convenience. Most programs account for PBC. Some 
don't. It is generally a safe practice to just make molecules whole as 
your first step in trjconv and avoid any ambiguity.


-Justin


Sent from my iPhone


On Jan 17, 2018, at 16:19, Justin Lemkul  wrote:




On 1/17/18 5:51 AM, Vidya R wrote:
Hi Justin,

I got the same result as you said.

What confused me was,  when I viewed movie.pdb file generated by the
following command,

  gmx trjconv -pbc nojump -s PRD-SMP3.gro -f PRD-SMP3.xtc -e 1.0 -n
index.ndx -o movie.pdb


two hydrogen molecules of my organic compound, were unbonded to my molecule
(which is not supposed to be).  They are far away from molecules (their
bonds were broken)

Is it a pbc problem?

Because, when I used

gmx trjconv -pbc whole -s PRD.tpr -f PRD.xtc -o trajwhole.xtc
gmx trjconv -pbc nojump -s PRD.tpr -f trajwhole.xtc -o trajcluster.xtc
gmx trjconv -pbc mol -center -s PRD.tpr -f trajcluster.xtc -o newtraj.xtc


and created a .pdb file with newtraj.xtc, the whole molecule was intact.

Making molecules whole should always be the first step. If you try to remove jumps with 
"broken" molecules, what you visualize will be garbage. A separate issue is 
with respect to the analysis programs - many are PBC-aware and can handle the original 
trajectory without manipulation.

-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

==

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--
==

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

==

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Re: [gmx-users] regarding pbc issue

[Rose]

You mean if -pbc could make molecule whole,everything is ok, but if not it 
means the molecule was broken from first, yes?

Sent from my iPhone

> On Jan 17, 2018, at 16:19, Justin Lemkul  wrote:
> 
> 
> 
>> On 1/17/18 5:51 AM, Vidya R wrote:
>> Hi Justin,
>> 
>> I got the same result as you said.
>> 
>> What confused me was,  when I viewed movie.pdb file generated by the
>> following command,
>> 
>>  gmx trjconv -pbc nojump -s PRD-SMP3.gro -f PRD-SMP3.xtc -e 1.0 -n
>> index.ndx -o movie.pdb
>> 
>> 
>> two hydrogen molecules of my organic compound, were unbonded to my molecule
>> (which is not supposed to be).  They are far away from molecules (their
>> bonds were broken)
>> 
>> Is it a pbc problem?
>> 
>> Because, when I used
>> 
>> gmx trjconv -pbc whole -s PRD.tpr -f PRD.xtc -o trajwhole.xtc
>> gmx trjconv -pbc nojump -s PRD.tpr -f trajwhole.xtc -o trajcluster.xtc
>> gmx trjconv -pbc mol -center -s PRD.tpr -f trajcluster.xtc -o newtraj.xtc
>> 
>> 
>> and created a .pdb file with newtraj.xtc, the whole molecule was intact.
> 
> Making molecules whole should always be the first step. If you try to remove 
> jumps with "broken" molecules, what you visualize will be garbage. A separate 
> issue is with respect to the analysis programs - many are PBC-aware and can 
> handle the original trajectory without manipulation.
> 
> -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
> 
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Re: [gmx-users] regarding pbc issue

[Justin Lemkul]

On 1/17/18 5:51 AM, Vidya R wrote:

Hi Justin,

I got the same result as you said.

What confused me was,  when I viewed movie.pdb file generated by the
following command,

  gmx trjconv -pbc nojump -s PRD-SMP3.gro -f PRD-SMP3.xtc -e 1.0 -n
index.ndx -o movie.pdb


two hydrogen molecules of my organic compound, were unbonded to my molecule
(which is not supposed to be).  They are far away from molecules (their
bonds were broken)

Is it a pbc problem?

Because, when I used

gmx trjconv -pbc whole -s PRD.tpr -f PRD.xtc -o trajwhole.xtc
gmx trjconv -pbc nojump -s PRD.tpr -f trajwhole.xtc -o trajcluster.xtc
gmx trjconv -pbc mol -center -s PRD.tpr -f trajcluster.xtc -o newtraj.xtc


and created a .pdb file with newtraj.xtc, the whole molecule was intact.


Making molecules whole should always be the first step. If you try to 
remove jumps with "broken" molecules, what you visualize will be 
garbage. A separate issue is with respect to the analysis programs - 
many are PBC-aware and can handle the original trajectory without 
manipulation.


-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
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Re: [gmx-users] regarding pbc issue

[Vidya R]

Hi Justin,

I got the same result as you said.

What confused me was,  when I viewed movie.pdb file generated by the
following command,

 gmx trjconv -pbc nojump -s PRD-SMP3.gro -f PRD-SMP3.xtc -e 1.0 -n
index.ndx -o movie.pdb


two hydrogen molecules of my organic compound, were unbonded to my molecule
(which is not supposed to be).  They are far away from molecules (their
bonds were broken)

Is it a pbc problem?

Because, when I used

gmx trjconv -pbc whole -s PRD.tpr -f PRD.xtc -o trajwhole.xtc
gmx trjconv -pbc nojump -s PRD.tpr -f trajwhole.xtc -o trajcluster.xtc
gmx trjconv -pbc mol -center -s PRD.tpr -f trajcluster.xtc -o newtraj.xtc


and created a .pdb file with newtraj.xtc, the whole molecule was intact.

Thanks,
Vidya.R



On Sat, Jan 13, 2018 at 7:25 PM, Justin Lemkul  wrote:

>
>
> On 1/13/18 7:53 AM, Vidya R wrote:
>
>> Hi gmx users,
>>
>> I used the following commands after simulation run (organic compound in
>> water, to calculate rdf)
>>
>>
>>
>>   gmx trjconv -pbc whole -s PRD.tpr -f PRD.xtc -o trajwhole.xtc
>> gmx trjconv -pbc nojump -s PRD.tpr -f trajwhole.xtc -o trajcluster.xtc
>>   gmx trjconv -pbc mol -center -s PRD.tpr -f trajcluster.xtc -o
>> newtraj.xtc
>>
>>
>> To use the following command, which xtc file should I use?
>>
>> gmx rdf -f ---.xtc -n index.ndx
>>
>> *prd or newtraj.xtc?*
>>
>> Please clear my doubt.
>>
>
> Run both and see if there is a difference. gmx rdf should be PBC-aware, so
> you should get the same result.
>
> -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
>
> ==
>
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> Gromacs Users mailing list
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Re: [gmx-users] regarding pbc issue

[Justin Lemkul]

On 1/13/18 7:53 AM, Vidya R wrote:

Hi gmx users,

I used the following commands after simulation run (organic compound in
water, to calculate rdf)



  gmx trjconv -pbc whole -s PRD.tpr -f PRD.xtc -o trajwhole.xtc
gmx trjconv -pbc nojump -s PRD.tpr -f trajwhole.xtc -o trajcluster.xtc
  gmx trjconv -pbc mol -center -s PRD.tpr -f trajcluster.xtc -o newtraj.xtc


To use the following command, which xtc file should I use?

gmx rdf -f ---.xtc -n index.ndx

*prd or newtraj.xtc?*

Please clear my doubt.


Run both and see if there is a difference. gmx rdf should be PBC-aware, 
so you should get the same result.


-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

==

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[gmx-users] regarding pbc issue

[Vidya R]

Hi gmx users,

I used the following commands after simulation run (organic compound in
water, to calculate rdf)



 gmx trjconv -pbc whole -s PRD.tpr -f PRD.xtc -o trajwhole.xtc
gmx trjconv -pbc nojump -s PRD.tpr -f trajwhole.xtc -o trajcluster.xtc
 gmx trjconv -pbc mol -center -s PRD.tpr -f trajcluster.xtc -o newtraj.xtc


To use the following command, which xtc file should I use?

gmx rdf -f ---.xtc -n index.ndx

*prd or newtraj.xtc?*

Please clear my doubt.

Thanks,

*Vidya.R*
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