subject:"\[gmx\-users\] trjconv"

You, my friend, are a genius. All worked, thanks tons.

Alex

On Mon, Apr 18, 2016 at 5:40 PM, Justin Lemkul  wrote:

>
>
> On 4/18/16 7:39 PM, Alex wrote:
>
>> The atom groups, as they appear in the coordinate input, are:
>>
>> 1. DNA atoms (labeled DA, DC, etc)
>> 2. CNT atoms
>> 3. SOL
>> 4. Ions
>>
>> I tried the following (prod.tpr and traj_comp.xtc are the original tpr and
>> compressed trajectory, respectively):
>>
>> step 1:
>>   gmx convert-tpr -s prod.tpr -o cnt_only.tpr
>> selected CNT
>> step 2:
>> trjconv -f traj_comp.xtc -s cnt_only.tpr -o test.pdb
>>
>> this last one does not even bother to open the menu, it throws the
>> following:
>>
>> ---
>> Program trjconv, VERSION 5.0.5
>> Source code file:
>> /home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxlib/mtop_util.c,
>> line:
>> 957
>>
>> Software inconsistency error:
>> Position restraint coordinates are missing
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> ---
>>
>> Any thoughts?
>>
>>
> You need to make:
>
> 1. New .tpr with no restraints
> 2. Subset .tpr with just the CNT
>
>
> -Justin
>
>
>>
>> On Mon, Apr 18, 2016 at 5:33 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 4/18/16 7:27 PM, Alex wrote:
>>>
>>> Yes, there are more atoms in the system, but only 2837 of them are
 labeled
 "CNT.' Well, I could share the files with you, of course, but you're
 running the latest version, aren't you? :)


 As you might expect, yes.
>>>
>>> Do the atom numbers of the CNT start from 1, or is there something else
>>> listed before it in the coordinates and topology?  If that's the case,
>>> making a matching .tpr via convert-tpr is the only option.
>>>
>>> -Justin
>>>
>>>
>>> On Mon, Apr 18, 2016 at 5:23 PM, Justin Lemkul  wrote:
>>>



> On 4/18/16 7:20 PM, Alex wrote:
>
> Justin,
>
>>
>> I understand what you're saying, but for the life of me I can't
>> understand
>> where this discrepancy is coming from, because the input coordinates
>> have
>> 2837 CNT atoms, and trjconv selector menu lists that number correctly.
>> Completely lost here. Are there any alternatives to output (in mdp)
>> the
>> correct group?
>>
>>
>> Without access to your files, there's nothing else I can really tell
>>
> you.
> Presumably there are more atoms in the system, yes?  Your index group
> somehow specifies out-of-range atoms.  Or maybe trjconv isn't parsing
> the
> .tpr properly (use convert-tpr to output a matching .tpr that has only
> CNT
> and try again).  I feel like there was an issue with this some time
> ago;
> 5.0.5 is considered old nowadays so the bug should have been fixed :)
>
> -Justin
>
>
> Alex
>
>
>> On Mon, Apr 18, 2016 at 5:15 PM, Justin Lemkul 
>> wrote:
>>
>>
>>
>> On 4/18/16 6:17 PM, Alex wrote:
>>>
>>> Hi all,
>>>
>>>
 I've got a system that includes a group named "CNT" consisting of
 2837
 atoms. To save space, I am outputting (at a very high rate) a
 compressed
 trajectory that contains only that group. The GMX version is 5.0.5.
 Here's
 the relevant mdp excerpt:


 nstxout =  1
 nstcomm =  1000
 nstxout-compressed  =  10
 compressed-x-grps   =  CNT
 nstvout =  1000
 nstfout =  500
 nstlog  =  100
 nstenergy   =  500
 nstlist =  20

 Upon trying to convert the compressed trajectory, after selecting
 the
 appropriate group from the menu (CNT, 2837 atoms), I get:

 command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb

 output:
 ---
 Program trjconv, VERSION 5.0.5
 Source code file:


 /home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c,
 line: 1330

 Fatal error:
 Index[2645] 2838 is larger than the number of atoms in the
 trajectory file (2837). There is a mismatch in the contents
 of your -f, -s and/or -n files.
 For more information and tips for troubleshooting, please check the
 GROMACS
 website at http://www.gromacs.org/Documentation/Errors

 Where's this single-atom discrepancy coming from? Any suggestions?


 Whatever you selected as output contains more atoms than are in the

 trajectory.  Note that it's not necessarily a single-atom
>>>

Re: [gmx-users] trjconv index mismatch




On 4/18/16 7:39 PM, Alex wrote:

The atom groups, as they appear in the coordinate input, are:

1. DNA atoms (labeled DA, DC, etc)
2. CNT atoms
3. SOL
4. Ions

I tried the following (prod.tpr and traj_comp.xtc are the original tpr and
compressed trajectory, respectively):

step 1:
  gmx convert-tpr -s prod.tpr -o cnt_only.tpr
selected CNT
step 2:
trjconv -f traj_comp.xtc -s cnt_only.tpr -o test.pdb

this last one does not even bother to open the menu, it throws the
following:

---
Program trjconv, VERSION 5.0.5
Source code file:
/home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxlib/mtop_util.c, line:
957

Software inconsistency error:
Position restraint coordinates are missing
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Any thoughts?



You need to make:

1. New .tpr with no restraints
2. Subset .tpr with just the CNT

-Justin




On Mon, Apr 18, 2016 at 5:33 PM, Justin Lemkul  wrote:




On 4/18/16 7:27 PM, Alex wrote:


Yes, there are more atoms in the system, but only 2837 of them are labeled
"CNT.' Well, I could share the files with you, of course, but you're
running the latest version, aren't you? :)



As you might expect, yes.

Do the atom numbers of the CNT start from 1, or is there something else
listed before it in the coordinates and topology?  If that's the case,
making a matching .tpr via convert-tpr is the only option.

-Justin


On Mon, Apr 18, 2016 at 5:23 PM, Justin Lemkul  wrote:





On 4/18/16 7:20 PM, Alex wrote:

Justin,


I understand what you're saying, but for the life of me I can't
understand
where this discrepancy is coming from, because the input coordinates
have
2837 CNT atoms, and trjconv selector menu lists that number correctly.
Completely lost here. Are there any alternatives to output (in mdp) the
correct group?


Without access to your files, there's nothing else I can really tell

you.
Presumably there are more atoms in the system, yes?  Your index group
somehow specifies out-of-range atoms.  Or maybe trjconv isn't parsing the
.tpr properly (use convert-tpr to output a matching .tpr that has only
CNT
and try again).  I feel like there was an issue with this some time ago;
5.0.5 is considered old nowadays so the bug should have been fixed :)

-Justin


Alex



On Mon, Apr 18, 2016 at 5:15 PM, Justin Lemkul  wrote:




On 4/18/16 6:17 PM, Alex wrote:

Hi all,



I've got a system that includes a group named "CNT" consisting of 2837
atoms. To save space, I am outputting (at a very high rate) a
compressed
trajectory that contains only that group. The GMX version is 5.0.5.
Here's
the relevant mdp excerpt:


nstxout =  1
nstcomm =  1000
nstxout-compressed  =  10
compressed-x-grps   =  CNT
nstvout =  1000
nstfout =  500
nstlog  =  100
nstenergy   =  500
nstlist =  20

Upon trying to convert the compressed trajectory, after selecting the
appropriate group from the menu (CNT, 2837 atoms), I get:

command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb

output:
---
Program trjconv, VERSION 5.0.5
Source code file:

/home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c,
line: 1330

Fatal error:
Index[2645] 2838 is larger than the number of atoms in the
trajectory file (2837). There is a mismatch in the contents
of your -f, -s and/or -n files.
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors

Where's this single-atom discrepancy coming from? Any suggestions?


Whatever you selected as output contains more atoms than are in the


trajectory.  Note that it's not necessarily a single-atom discrepancy,
it's
just that the fatal error is triggered as soon as an index that is out
of
range is identified.  You're only outputting CNT, and presumably the
.tpr
contains more atoms, so the selection you're making can only be CNT or
some
subset of those atoms.

-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
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send a mail to

Re: [gmx-users] trjconv index mismatch

The atom groups, as they appear in the coordinate input, are:

1. DNA atoms (labeled DA, DC, etc)
2. CNT atoms
3. SOL
4. Ions

I tried the following (prod.tpr and traj_comp.xtc are the original tpr and
compressed trajectory, respectively):

step 1:
 gmx convert-tpr -s prod.tpr -o cnt_only.tpr
selected CNT
step 2:
trjconv -f traj_comp.xtc -s cnt_only.tpr -o test.pdb

this last one does not even bother to open the menu, it throws the
following:

---
Program trjconv, VERSION 5.0.5
Source code file:
/home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxlib/mtop_util.c, line:
957

Software inconsistency error:
Position restraint coordinates are missing
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Any thoughts?



On Mon, Apr 18, 2016 at 5:33 PM, Justin Lemkul  wrote:

>
>
> On 4/18/16 7:27 PM, Alex wrote:
>
>> Yes, there are more atoms in the system, but only 2837 of them are labeled
>> "CNT.' Well, I could share the files with you, of course, but you're
>> running the latest version, aren't you? :)
>>
>>
> As you might expect, yes.
>
> Do the atom numbers of the CNT start from 1, or is there something else
> listed before it in the coordinates and topology?  If that's the case,
> making a matching .tpr via convert-tpr is the only option.
>
> -Justin
>
>
> On Mon, Apr 18, 2016 at 5:23 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 4/18/16 7:20 PM, Alex wrote:
>>>
>>> Justin,

 I understand what you're saying, but for the life of me I can't
 understand
 where this discrepancy is coming from, because the input coordinates
 have
 2837 CNT atoms, and trjconv selector menu lists that number correctly.
 Completely lost here. Are there any alternatives to output (in mdp) the
 correct group?


 Without access to your files, there's nothing else I can really tell
>>> you.
>>> Presumably there are more atoms in the system, yes?  Your index group
>>> somehow specifies out-of-range atoms.  Or maybe trjconv isn't parsing the
>>> .tpr properly (use convert-tpr to output a matching .tpr that has only
>>> CNT
>>> and try again).  I feel like there was an issue with this some time ago;
>>> 5.0.5 is considered old nowadays so the bug should have been fixed :)
>>>
>>> -Justin
>>>
>>>
>>> Alex
>>>

 On Mon, Apr 18, 2016 at 5:15 PM, Justin Lemkul  wrote:



> On 4/18/16 6:17 PM, Alex wrote:
>
> Hi all,
>
>>
>> I've got a system that includes a group named "CNT" consisting of 2837
>> atoms. To save space, I am outputting (at a very high rate) a
>> compressed
>> trajectory that contains only that group. The GMX version is 5.0.5.
>> Here's
>> the relevant mdp excerpt:
>>
>>
>> nstxout =  1
>> nstcomm =  1000
>> nstxout-compressed  =  10
>> compressed-x-grps   =  CNT
>> nstvout =  1000
>> nstfout =  500
>> nstlog  =  100
>> nstenergy   =  500
>> nstlist =  20
>>
>> Upon trying to convert the compressed trajectory, after selecting the
>> appropriate group from the menu (CNT, 2837 atoms), I get:
>>
>> command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb
>>
>> output:
>> ---
>> Program trjconv, VERSION 5.0.5
>> Source code file:
>>
>> /home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c,
>> line: 1330
>>
>> Fatal error:
>> Index[2645] 2838 is larger than the number of atoms in the
>> trajectory file (2837). There is a mismatch in the contents
>> of your -f, -s and/or -n files.
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>> Where's this single-atom discrepancy coming from? Any suggestions?
>>
>>
>> Whatever you selected as output contains more atoms than are in the
>>
> trajectory.  Note that it's not necessarily a single-atom discrepancy,
> it's
> just that the fatal error is triggered as soon as an index that is out
> of
> range is identified.  You're only outputting CNT, and presumably the
> .tpr
> contains more atoms, so the selection you're making can only be CNT or
> some
> subset of those atoms.
>
> -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.
>

Re: [gmx-users] trjconv index mismatch




On 4/18/16 7:27 PM, Alex wrote:

Yes, there are more atoms in the system, but only 2837 of them are labeled
"CNT.' Well, I could share the files with you, of course, but you're
running the latest version, aren't you? :)



As you might expect, yes.

Do the atom numbers of the CNT start from 1, or is there something else listed 
before it in the coordinates and topology?  If that's the case, making a 
matching .tpr via convert-tpr is the only option.


-Justin


On Mon, Apr 18, 2016 at 5:23 PM, Justin Lemkul  wrote:




On 4/18/16 7:20 PM, Alex wrote:


Justin,

I understand what you're saying, but for the life of me I can't understand
where this discrepancy is coming from, because the input coordinates have
2837 CNT atoms, and trjconv selector menu lists that number correctly.
Completely lost here. Are there any alternatives to output (in mdp) the
correct group?



Without access to your files, there's nothing else I can really tell you.
Presumably there are more atoms in the system, yes?  Your index group
somehow specifies out-of-range atoms.  Or maybe trjconv isn't parsing the
.tpr properly (use convert-tpr to output a matching .tpr that has only CNT
and try again).  I feel like there was an issue with this some time ago;
5.0.5 is considered old nowadays so the bug should have been fixed :)

-Justin


Alex


On Mon, Apr 18, 2016 at 5:15 PM, Justin Lemkul  wrote:




On 4/18/16 6:17 PM, Alex wrote:

Hi all,


I've got a system that includes a group named "CNT" consisting of 2837
atoms. To save space, I am outputting (at a very high rate) a compressed
trajectory that contains only that group. The GMX version is 5.0.5.
Here's
the relevant mdp excerpt:


nstxout =  1
nstcomm =  1000
nstxout-compressed  =  10
compressed-x-grps   =  CNT
nstvout =  1000
nstfout =  500
nstlog  =  100
nstenergy   =  500
nstlist =  20

Upon trying to convert the compressed trajectory, after selecting the
appropriate group from the menu (CNT, 2837 atoms), I get:

command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb

output:
---
Program trjconv, VERSION 5.0.5
Source code file:
/home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c,
line: 1330

Fatal error:
Index[2645] 2838 is larger than the number of atoms in the
trajectory file (2837). There is a mismatch in the contents
of your -f, -s and/or -n files.
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors

Where's this single-atom discrepancy coming from? Any suggestions?


Whatever you selected as output contains more atoms than are in the

trajectory.  Note that it's not necessarily a single-atom discrepancy,
it's
just that the fatal error is triggered as soon as an index that is out of
range is identified.  You're only outputting CNT, and presumably the .tpr
contains more atoms, so the selection you're making can only be CNT or
some
subset of those atoms.

-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.



--
==

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.



--
==

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

Re: [gmx-users] trjconv index mismatch

Yes, there are more atoms in the system, but only 2837 of them are labeled
"CNT.' Well, I could share the files with you, of course, but you're
running the latest version, aren't you? :)

On Mon, Apr 18, 2016 at 5:23 PM, Justin Lemkul  wrote:

>
>
> On 4/18/16 7:20 PM, Alex wrote:
>
>> Justin,
>>
>> I understand what you're saying, but for the life of me I can't understand
>> where this discrepancy is coming from, because the input coordinates have
>> 2837 CNT atoms, and trjconv selector menu lists that number correctly.
>> Completely lost here. Are there any alternatives to output (in mdp) the
>> correct group?
>>
>>
> Without access to your files, there's nothing else I can really tell you.
> Presumably there are more atoms in the system, yes?  Your index group
> somehow specifies out-of-range atoms.  Or maybe trjconv isn't parsing the
> .tpr properly (use convert-tpr to output a matching .tpr that has only CNT
> and try again).  I feel like there was an issue with this some time ago;
> 5.0.5 is considered old nowadays so the bug should have been fixed :)
>
> -Justin
>
>
> Alex
>>
>> On Mon, Apr 18, 2016 at 5:15 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 4/18/16 6:17 PM, Alex wrote:
>>>
>>> Hi all,

 I've got a system that includes a group named "CNT" consisting of 2837
 atoms. To save space, I am outputting (at a very high rate) a compressed
 trajectory that contains only that group. The GMX version is 5.0.5.
 Here's
 the relevant mdp excerpt:


 nstxout =  1
 nstcomm =  1000
 nstxout-compressed  =  10
 compressed-x-grps   =  CNT
 nstvout =  1000
 nstfout =  500
 nstlog  =  100
 nstenergy   =  500
 nstlist =  20

 Upon trying to convert the compressed trajectory, after selecting the
 appropriate group from the menu (CNT, 2837 atoms), I get:

 command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb

 output:
 ---
 Program trjconv, VERSION 5.0.5
 Source code file:
 /home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c,
 line: 1330

 Fatal error:
 Index[2645] 2838 is larger than the number of atoms in the
 trajectory file (2837). There is a mismatch in the contents
 of your -f, -s and/or -n files.
 For more information and tips for troubleshooting, please check the
 GROMACS
 website at http://www.gromacs.org/Documentation/Errors

 Where's this single-atom discrepancy coming from? Any suggestions?


 Whatever you selected as output contains more atoms than are in the
>>> trajectory.  Note that it's not necessarily a single-atom discrepancy,
>>> it's
>>> just that the fatal error is triggered as soon as an index that is out of
>>> range is identified.  You're only outputting CNT, and presumably the .tpr
>>> contains more atoms, so the selection you're making can only be CNT or
>>> some
>>> subset of those atoms.
>>>
>>> -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.
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at

Re: [gmx-users] trjconv index mismatch




On 4/18/16 7:20 PM, Alex wrote:

Justin,

I understand what you're saying, but for the life of me I can't understand
where this discrepancy is coming from, because the input coordinates have
2837 CNT atoms, and trjconv selector menu lists that number correctly.
Completely lost here. Are there any alternatives to output (in mdp) the
correct group?



Without access to your files, there's nothing else I can really tell you. 
Presumably there are more atoms in the system, yes?  Your index group somehow 
specifies out-of-range atoms.  Or maybe trjconv isn't parsing the .tpr properly 
(use convert-tpr to output a matching .tpr that has only CNT and try again).  I 
feel like there was an issue with this some time ago; 5.0.5 is considered old 
nowadays so the bug should have been fixed :)


-Justin


Alex

On Mon, Apr 18, 2016 at 5:15 PM, Justin Lemkul  wrote:




On 4/18/16 6:17 PM, Alex wrote:


Hi all,

I've got a system that includes a group named "CNT" consisting of 2837
atoms. To save space, I am outputting (at a very high rate) a compressed
trajectory that contains only that group. The GMX version is 5.0.5. Here's
the relevant mdp excerpt:


nstxout =  1
nstcomm =  1000
nstxout-compressed  =  10
compressed-x-grps   =  CNT
nstvout =  1000
nstfout =  500
nstlog  =  100
nstenergy   =  500
nstlist =  20

Upon trying to convert the compressed trajectory, after selecting the
appropriate group from the menu (CNT, 2837 atoms), I get:

command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb

output:
---
Program trjconv, VERSION 5.0.5
Source code file:
/home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c,
line: 1330

Fatal error:
Index[2645] 2838 is larger than the number of atoms in the
trajectory file (2837). There is a mismatch in the contents
of your -f, -s and/or -n files.
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors

Where's this single-atom discrepancy coming from? Any suggestions?



Whatever you selected as output contains more atoms than are in the
trajectory.  Note that it's not necessarily a single-atom discrepancy, it's
just that the fatal error is triggered as soon as an index that is out of
range is identified.  You're only outputting CNT, and presumably the .tpr
contains more atoms, so the selection you're making can only be CNT or some
subset of those atoms.

-Justin

--
==

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

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

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

==
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--
==

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

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http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] trjconv index mismatch




On 4/18/16 6:17 PM, Alex wrote:

Hi all,

I've got a system that includes a group named "CNT" consisting of 2837
atoms. To save space, I am outputting (at a very high rate) a compressed
trajectory that contains only that group. The GMX version is 5.0.5. Here's
the relevant mdp excerpt:


nstxout =  1
nstcomm =  1000
nstxout-compressed  =  10
compressed-x-grps   =  CNT
nstvout =  1000
nstfout =  500
nstlog  =  100
nstenergy   =  500
nstlist =  20

Upon trying to convert the compressed trajectory, after selecting the
appropriate group from the menu (CNT, 2837 atoms), I get:

command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb

output:
---
Program trjconv, VERSION 5.0.5
Source code file:
/home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c,
line: 1330

Fatal error:
Index[2645] 2838 is larger than the number of atoms in the
trajectory file (2837). There is a mismatch in the contents
of your -f, -s and/or -n files.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Where's this single-atom discrepancy coming from? Any suggestions?



Whatever you selected as output contains more atoms than are in the trajectory. 
 Note that it's not necessarily a single-atom discrepancy, it's just that the 
fatal error is triggered as soon as an index that is out of range is identified. 
 You're only outputting CNT, and presumably the .tpr contains more atoms, so 
the selection you're making can only be CNT or some subset of those atoms.


-Justin

--
==

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

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

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

==
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Re: [gmx-users] trjconv index mismatch

2016-04-18 Thread Juan Manuel Aceves-Hernandez

Dear all, is there an international workshop about Gromacs in America or
Europe the near future?.


2016-04-18 17:17 GMT-05:00 Alex :

> Hi all,
>
> I've got a system that includes a group named "CNT" consisting of 2837
> atoms. To save space, I am outputting (at a very high rate) a compressed
> trajectory that contains only that group. The GMX version is 5.0.5. Here's
> the relevant mdp excerpt:
>
>
> nstxout =  1
> nstcomm =  1000
> nstxout-compressed  =  10
> compressed-x-grps   =  CNT
> nstvout =  1000
> nstfout =  500
> nstlog  =  100
> nstenergy   =  500
> nstlist =  20
>
> Upon trying to convert the compressed trajectory, after selecting the
> appropriate group from the menu (CNT, 2837 atoms), I get:
>
> command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb
>
> output:
> ---
> Program trjconv, VERSION 5.0.5
> Source code file:
> /home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c,
> line: 1330
>
> Fatal error:
> Index[2645] 2838 is larger than the number of atoms in the
> trajectory file (2837). There is a mismatch in the contents
> of your -f, -s and/or -n files.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> Where's this single-atom discrepancy coming from? Any suggestions?
>
> Thanks,
>
> Alex
> --
> Gromacs Users mailing list
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> * Please search the archive at
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> posting!
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>



-- 
Juan Manuel Aceves Hernández
Laboratorio de Nanomateriales
Tel. 52 55 5623 1999 ext 39431
Tel y Fax 5623 20 68
Unidad de Investigación Multidisciplinaria
Campo 4, Facultad de Estudios Superiores Cuautitlan
Universidad Nacional Autonoma de México
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[gmx-users] trjconv index mismatch

Hi all,

I've got a system that includes a group named "CNT" consisting of 2837
atoms. To save space, I am outputting (at a very high rate) a compressed
trajectory that contains only that group. The GMX version is 5.0.5. Here's
the relevant mdp excerpt:


nstxout =  1
nstcomm =  1000
nstxout-compressed  =  10
compressed-x-grps   =  CNT
nstvout =  1000
nstfout =  500
nstlog  =  100
nstenergy   =  500
nstlist =  20

Upon trying to convert the compressed trajectory, after selecting the
appropriate group from the menu (CNT, 2837 atoms), I get:

command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb

output:
---
Program trjconv, VERSION 5.0.5
Source code file:
/home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c,
line: 1330

Fatal error:
Index[2645] 2838 is larger than the number of atoms in the
trajectory file (2837). There is a mismatch in the contents
of your -f, -s and/or -n files.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Where's this single-atom discrepancy coming from? Any suggestions?

Thanks,

Alex
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Re: [gmx-users] trjconv options?

2016-02-04 Thread Justin Lemkul

On 2/4/16 4:27 AM, Timofey Tyugashev wrote:

Message: 2
Date: Wed, 3 Feb 2016 07:37:42 -0500
From: Justin Lemkul<jalem...@vt.edu>
To:gmx-us...@gromacs.org
Subject: Re: [gmx-users] trjconv options?
Message-ID:<56b1f496.5090...@vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

On 2/3/16 6:34 AM, Timofey Tyugashev wrote:

>Thank you for replies on my previous questions.
>And now I have another one dealing with trjconv.
>
>I have a simulation of  a three-chain protein/nucleic acid complex. Naturally,
>it gets broken in three separate strands by PBC.
>After trying several, I settled on using options '-pbc mol' with '-ur compact'
>which makes the complex look decent again and it looks like that does the job.
>But I'm worried about a possibility of something getting unrepaired by this
>option and getting unnoticed by me. What is the way to check for it?

Any molecules that appear to fly away suddenly will be a pretty dead giveaway.

In general, for multimeric complexes, you need to do a lot more work, e.g.
centering on a single chain after making molecules whole and removing jumps.  If
a simple -pbc mol -ur compact does the trick, probably nothing has actually
crossed a periodic boundary yet.

>Also it keeps tumbling around the cell during the trajectory. It's annoying. Is
>there a way to pin down the cluster and stop it from rotating?

This is what trjconv -fit is for.

-Justin

Well, both vmd and pymol render .gro file (and trajectory files) with DNA
strands and protein positioned in different corners of the box.
Also, editconf -pbc has no effect on .gro file with the broken complex. How it's
supposed to behave?

So in this case I should at first run trjconv with '-pbc whole', make second run
with '-pbc nojump', then make third run with '-pbc mol' to properly repair the
trajectory?
I guess for -fit I should pick 'progressive' option?

Complex systems require complex operations.  Start with 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow 
because that order of operations generally works well.  Then see posts in the 
archive, because this comes up frequently.  Typically, after making molecules 
whole and removing jumps, you can center on a custom index group that defines 
some useful center.  Then you can do whatever fitting you like.

-Justin

--
==

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

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

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

==
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Re: [gmx-users] trjconv options?

2016-02-04 Thread Timofey Tyugashev

Message: 2
Date: Wed, 3 Feb 2016 07:37:42 -0500
From: Justin Lemkul<jalem...@vt.edu>
To:gmx-us...@gromacs.org
Subject: Re: [gmx-users] trjconv options?
Message-ID:<56b1f496.5090...@vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

On 2/3/16 6:34 AM, Timofey Tyugashev wrote:

>Thank you for replies on my previous questions.
>And now I have another one dealing with trjconv.
>
>I have a simulation of  a three-chain protein/nucleic acid complex. Naturally,
>it gets broken in three separate strands by PBC.
>After trying several, I settled on using options '-pbc mol' with '-ur compact'
>which makes the complex look decent again and it looks like that does the job.
>But I'm worried about a possibility of something getting unrepaired by this
>option and getting unnoticed by me. What is the way to check for it?

Any molecules that appear to fly away suddenly will be a pretty dead giveaway.

In general, for multimeric complexes, you need to do a lot more work, e.g.
centering on a single chain after making molecules whole and removing jumps.  If
a simple -pbc mol -ur compact does the trick, probably nothing has actually
crossed a periodic boundary yet.

>Also it keeps tumbling around the cell during the trajectory. It's annoying. Is
>there a way to pin down the cluster and stop it from rotating?

This is what trjconv -fit is for.

-Justin
Well, both vmd and pymol render .gro file (and trajectory files) with 
DNA strands and protein positioned in different corners of the box.
Also, editconf -pbc has no effect on .gro file with the broken complex. 
How it's supposed to behave?

So in this case I should at first run trjconv with '-pbc whole', make 
second run with '-pbc nojump', then make third run with '-pbc mol' to 
properly repair the trajectory?

I guess for -fit I should pick 'progressive' option?
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Re: [gmx-users] trjconv - two chains are separated

2016-02-03 Thread Catarina A. Carvalheda dos Santos

Hi there,

I had similar problems in the past. You'll have to play with trjconv and
find the best combination of different flags to solve the visualization
problem.

You can start by trying out this workflow for example:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Hope this helps.

Good luck!



On 3 February 2016 at 06:15, Trayder Thomas 
wrote:

> For "-pbc nojump" to work, you need to make sure they are together (as you
> want) in the first frame of your input trajectory.
>
> The most reliable way to do this is by centering the trajectory on a
> residue at the interface between the two chains (using a custom index
> group).
>
> I've also heard some people have had luck with "-pbc cluster"
>
> You can then run "-pbc nojump" on the centered (or clustered) trajectory.
>
> -Trayder
>
>
>
>
> On Wed, Feb 3, 2016 at 9:37 AM, Yunlong Liu  wrote:
>
> > Hi Gromacs Users,
> >
> > I used "gmx trjconv" (Gromacs 5.0.4) to remove the pbc of my
> trajectories.
> > My protein has two chains (A and B) and they closely bind to each other.
> > after running trjconv with "-pbc nojump", two chains are greatly
> separated
> > by a certain distance. It is mostly likely that the pbc is not
> successfully
> > removed and the program takes a chain from one unit cell and another from
> > another unit cell.
> >
> > Does anybody have any idea to solve the problem?
> >
> > Best
> > Yunlong
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>



-- 
Catarina A. Carvalheda

PhD Student
Computational Biology Division
SLS & SSE
University of Dundee
DD1 5EH, Dundee, Scotland, UK
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Re: [gmx-users] trjconv options?

2016-02-03 Thread Justin Lemkul




On 2/3/16 6:34 AM, Timofey Tyugashev wrote:

Thank you for replies on my previous questions.
And now I have another one dealing with trjconv.

I have a simulation of  a three-chain protein/nucleic acid complex. Naturally,
it gets broken in three separate strands by PBC.
After trying several, I settled on using options '-pbc mol' with '-ur compact'
which makes the complex look decent again and it looks like that does the job.
But I'm worried about a possibility of something getting unrepaired by this
option and getting unnoticed by me. What is the way to check for it?


Any molecules that appear to fly away suddenly will be a pretty dead giveaway.

In general, for multimeric complexes, you need to do a lot more work, e.g. 
centering on a single chain after making molecules whole and removing jumps.  If 
a simple -pbc mol -ur compact does the trick, probably nothing has actually 
crossed a periodic boundary yet.



Also it keeps tumbling around the cell during the trajectory. It's annoying. Is
there a way to pin down the cluster and stop it from rotating?


This is what trjconv -fit is for.

-Justin

--
==

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

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

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

==
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[gmx-users] trjconv options?

2016-02-03 Thread Timofey Tyugashev


Thank you for replies on my previous questions.
And now I have another one dealing with trjconv.

I have a simulation of  a three-chain protein/nucleic acid complex. 
Naturally, it gets broken in three separate strands by PBC.
After trying several, I settled on using options '-pbc mol' with '-ur 
compact' which makes the complex look decent again and it looks like 
that does the job.
But I'm worried about a possibility of something getting unrepaired by 
this option and getting unnoticed by me. What is the way to check for it?
Also it keeps tumbling around the cell during the trajectory. It's 
annoying. Is there a way to pin down the cluster and stop it from rotating?

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Re: [gmx-users] trjconv - two chains are separated

2016-02-03 Thread Peter Stern

I have also encountered this problem and was able to solve it using the tpr 
file generated before running editconf as the input to trjconv (with -pbc no 
jump).

Peter

Sent from my iPad

> On 3 בפבר׳ 2016, at 4:51, Catarina A. Carvalheda dos Santos 
>  wrote:
> 
> Hi there,
> 
> I had similar problems in the past. You'll have to play with trjconv and
> find the best combination of different flags to solve the visualization
> problem.
> 
> You can start by trying out this workflow for example:
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> 
> Hope this helps.
> 
> Good luck!
> 
> 
> 
> On 3 February 2016 at 06:15, Trayder Thomas 
> wrote:
> 
>> For "-pbc nojump" to work, you need to make sure they are together (as you
>> want) in the first frame of your input trajectory.
>> 
>> The most reliable way to do this is by centering the trajectory on a
>> residue at the interface between the two chains (using a custom index
>> group).
>> 
>> I've also heard some people have had luck with "-pbc cluster"
>> 
>> You can then run "-pbc nojump" on the centered (or clustered) trajectory.
>> 
>> -Trayder
>> 
>> 
>> 
>> 
>>> On Wed, Feb 3, 2016 at 9:37 AM, Yunlong Liu  wrote:
>>> 
>>> Hi Gromacs Users,
>>> 
>>> I used "gmx trjconv" (Gromacs 5.0.4) to remove the pbc of my
>> trajectories.
>>> My protein has two chains (A and B) and they closely bind to each other.
>>> after running trjconv with "-pbc nojump", two chains are greatly
>> separated
>>> by a certain distance. It is mostly likely that the pbc is not
>> successfully
>>> removed and the program takes a chain from one unit cell and another from
>>> another unit cell.
>>> 
>>> Does anybody have any idea to solve the problem?
>>> 
>>> Best
>>> Yunlong
>>> --
>>> 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.
>> --
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>> posting!
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>> send a mail to gmx-users-requ...@gromacs.org.
>> 
>> The University of Dundee is a registered Scottish Charity, No: SC015096
> 
> 
> 
> -- 
> Catarina A. Carvalheda
> 
> PhD Student
> Computational Biology Division
> SLS & SSE
> University of Dundee
> DD1 5EH, Dundee, Scotland, UK
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[gmx-users] trjconv - two chains are separated

2016-02-02 Thread Yunlong Liu


Hi Gromacs Users,

I used "gmx trjconv" (Gromacs 5.0.4) to remove the pbc of my 
trajectories. My protein has two chains (A and B) and they closely bind 
to each other. after running trjconv with "-pbc nojump", two chains are 
greatly separated by a certain distance. It is mostly likely that the 
pbc is not successfully removed and the program takes a chain from one 
unit cell and another from another unit cell.


Does anybody have any idea to solve the problem?

Best
Yunlong
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Re: [gmx-users] trjconv - two chains are separated

2016-02-02 Thread Trayder Thomas

For "-pbc nojump" to work, you need to make sure they are together (as you
want) in the first frame of your input trajectory.

The most reliable way to do this is by centering the trajectory on a
residue at the interface between the two chains (using a custom index
group).

I've also heard some people have had luck with "-pbc cluster"

You can then run "-pbc nojump" on the centered (or clustered) trajectory.

-Trayder

On Wed, Feb 3, 2016 at 9:37 AM, Yunlong Liu  wrote:

> Hi Gromacs Users,
>
> I used "gmx trjconv" (Gromacs 5.0.4) to remove the pbc of my trajectories.
> My protein has two chains (A and B) and they closely bind to each other.
> after running trjconv with "-pbc nojump", two chains are greatly separated
> by a certain distance. It is mostly likely that the pbc is not successfully
> removed and the program takes a chain from one unit cell and another from
> another unit cell.
>
> Does anybody have any idea to solve the problem?
>
> Best
> Yunlong
> --
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[gmx-users] trjconv -pbc nojump

Hi,


I want to use trjconv -pbc nojump to create a trajectory without box jumping of 
molecules. The molecules (lipids) also start to diffuse out of the box like 
they should, but in some a part of the molecule still jumps (as I could observe 
in xy direction), while the rest doesn't, leading to artificially long bonds in 
VMD. I tried trjconv -pbc nojump both with a tpr file in the -s option, or a 
gro file (with only complete molecules), same result.


I'd be glad if somebody could give me a hint.


Cheers

Sabine



--
Dr. Sabine Reißer
Theoretical Chemical Biology
Institute of Physical Chemistry
Karlsruhe Institute of Technology

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Re: [gmx-users] trjconv -pbc nojump

2015-09-02 Thread Justin Lemkul




On 9/2/15 9:36 AM, Reisser, Sabine (IPC) wrote:

Well, in the end I would like to have an average value for the P atoms of
each leaflet. I know which lipids belong to which leaflet, but I need to
avoid box jumps along z, otherwise I will obviously get a wrong average.
Using first trjconv  -pbc whole and then -pbc nojump actually seems to work
in the way that molecules don't jump in z anymore. However, they are not
whole anymore. Also, I would like all lipids of one leaflet on one side of


Once made whole, I don't understand how they would have further problems.  Make 
sure your reference structure in the .tpr passed to -s has whole molecules that 
are all in the box as a proper reference.



the box. Now, the lipids upper edge is at the box edge, and some have jumped
to the lower box edge. I thought maybe with -pbc cluster I could fix this.
Otherwise I have to shift the molecules which are jumped (already in the
starting structure) manually by the box height.



This can be overcome with the -trans (in concert with -pbc mol) and/or -center 
options.


-Justin

--
==

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

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

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

==
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Re: [gmx-users] trjconv -pbc nojump

Thanks for the reply, but I don't want the lipids to jump from one edge of the 
box to the other, which they do with this option, even though they remain 
complete.

Cheers
Sabine

--
Dr. Sabine Reißer
Theoretical Chemical Biology
Institute of Physical Chemistry
Karlsruhe Institute of Technology

Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> im Auftrag von Ganesh 
Shahane <ganesh7shah...@gmail.com>
Gesendet: Mittwoch, 2. September 2015 12:19
An: gmx-us...@gromacs.org
Betreff: Re: [gmx-users] trjconv -pbc nojump

Hi Reisser,

Instead of using -pbc nojump, use -pbc whole.

On Wed, Sep 2, 2015 at 2:47 PM, Reisser, Sabine (IPC) <
sabine.reis...@kit.edu> wrote:

> Hi,
>
>
> I want to use trjconv -pbc nojump to create a trajectory without box
> jumping of molecules. The molecules (lipids) also start to diffuse out of
> the box like they should, but in some a part of the molecule still jumps
> (as I could observe in xy direction), while the rest doesn't, leading to
> artificially long bonds in VMD. I tried trjconv -pbc nojump both with a tpr
> file in the -s option, or a gro file (with only complete molecules), same
> result.
>
>
> I'd be glad if somebody could give me a hint.
>
>
> Cheers
>
> Sabine
>
>
>
> --
> Dr. Sabine Reißer
> Theoretical Chemical Biology
> Institute of Physical Chemistry
> Karlsruhe Institute of Technology
>
> --
> 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.
>

--
Best Regards,
Ganesh Shahane
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Re: [gmx-users] trjconv -pbc nojump

Well, in the end I would like to have an average value for the P atoms of each 
leaflet. I know which lipids belong to which leaflet, but I need to avoid box 
jumps along z, otherwise I will obviously get a wrong average.
Using first trjconv  -pbc whole and then -pbc nojump actually seems to work in 
the way that molecules don't jump in z anymore. However, they are not whole 
anymore. 
Also, I would like all lipids of one leaflet on one side of the box. Now, the 
lipids upper edge is at the box edge, and some have jumped to the lower box 
edge. I thought maybe with -pbc cluster I could fix this. Otherwise I have to 
shift the molecules which are jumped (already in the starting structure) 
manually by the box height.

Cheers
Sabine

--
Dr. Sabine Reißer
Theoretical Chemical Biology
Institute of Physical Chemistry
Karlsruhe Institute of Technology



Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> im Auftrag von Justin 
Lemkul <jalem...@vt.edu>
Gesendet: Mittwoch, 2. September 2015 15:06
An: gmx-us...@gromacs.org
Betreff: Re: [gmx-users] trjconv -pbc nojump

On 9/2/15 9:04 AM, Reisser, Sabine (IPC) wrote:
> Thanks, I made them whole and tried to cluster the lipids with -pbc cluster.
> However, I keep getting a Fatal error:
> Molecule 1 marked for clustering but not atom 1 in it - check your index!
>
> This happens no matter which index group I use.
> Do you have any ideas what's the reason?
>

Does it even make sense to try to cluster these molecules?  Note that not every
step on that list is needed.

-Justin

> Cheers
> Sabine
>
>
> --
> Dr. Sabine Reißer
> Theoretical Chemical Biology
> Institute of Physical Chemistry
> Karlsruhe Institute of Technology
>
>
> 
> Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
> <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> im Auftrag von Justin 
> Lemkul <jalem...@vt.edu>
> Gesendet: Mittwoch, 2. September 2015 14:13
> An: gmx-us...@gromacs.org
> Betreff: Re: [gmx-users] trjconv -pbc nojump
>
> On 9/2/15 7:17 AM, Reisser, Sabine (IPC) wrote:
>> Thanks for the reply, but I don't want the lipids to jump from one edge of 
>> the box to the other, which they do with this option, even though they 
>> remain complete.
>>
>
> Making molecules whole should be the first step, followed by removing jumps.
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
>
> -Justin
>
>> Cheers
>> Sabine
>>
>>
>>
>> --
>> Dr. Sabine Reißer
>> Theoretical Chemical Biology
>> Institute of Physical Chemistry
>> Karlsruhe Institute of Technology
>>
>>
>> 
>> Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>> <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> im Auftrag von Ganesh 
>> Shahane <ganesh7shah...@gmail.com>
>> Gesendet: Mittwoch, 2. September 2015 12:19
>> An: gmx-us...@gromacs.org
>> Betreff: Re: [gmx-users] trjconv -pbc nojump
>>
>> Hi Reisser,
>>
>> Instead of using -pbc nojump, use -pbc whole.
>>
>> On Wed, Sep 2, 2015 at 2:47 PM, Reisser, Sabine (IPC) <
>> sabine.reis...@kit.edu> wrote:
>>
>>> Hi,
>>>
>>>
>>> I want to use trjconv -pbc nojump to create a trajectory without box
>>> jumping of molecules. The molecules (lipids) also start to diffuse out of
>>> the box like they should, but in some a part of the molecule still jumps
>>> (as I could observe in xy direction), while the rest doesn't, leading to
>>> artificially long bonds in VMD. I tried trjconv -pbc nojump both with a tpr
>>> file in the -s option, or a gro file (with only complete molecules), same
>>> result.
>>>
>>>
>>> I'd be glad if somebody could give me a hint.
>>>
>>>
>>> Cheers
>>>
>>> Sabine
>>>
>>>
>>>
>>> --
>>> Dr. Sabine Reißer
>>> Theoretical Chemical Biology
>>> Institute of Physical Chemistry
>>> Karlsruhe Institute of Technology
>>>
>>> --
>>> 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
>>

Re: [gmx-users] trjconv -pbc nojump

2015-09-02 Thread Ganesh Shahane

Hi Reisser,

Instead of using -pbc nojump, use -pbc whole.

On Wed, Sep 2, 2015 at 2:47 PM, Reisser, Sabine (IPC) <
sabine.reis...@kit.edu> wrote:

> Hi,
>
>
> I want to use trjconv -pbc nojump to create a trajectory without box
> jumping of molecules. The molecules (lipids) also start to diffuse out of
> the box like they should, but in some a part of the molecule still jumps
> (as I could observe in xy direction), while the rest doesn't, leading to
> artificially long bonds in VMD. I tried trjconv -pbc nojump both with a tpr
> file in the -s option, or a gro file (with only complete molecules), same
> result.
>
>
> I'd be glad if somebody could give me a hint.
>
>
> Cheers
>
> Sabine
>
>
>
> --
> Dr. Sabine Reißer
> Theoretical Chemical Biology
> Institute of Physical Chemistry
> Karlsruhe Institute of Technology
>
> --
> 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.
>



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Ganesh Shahane
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Re: [gmx-users] trjconv -pbc nojump

2015-09-02 Thread Justin Lemkul

On 9/2/15 9:04 AM, Reisser, Sabine (IPC) wrote:

Thanks, I made them whole and tried to cluster the lipids with -pbc cluster.
However, I keep getting a Fatal error:
Molecule 1 marked for clustering but not atom 1 in it - check your index!

This happens no matter which index group I use.
Do you have any ideas what's the reason?

Does it even make sense to try to cluster these molecules? Note that not every
step on that list is needed.

-Justin

Cheers
Sabine

--
Dr. Sabine Reißer
Theoretical Chemical Biology
Institute of Physical Chemistry
Karlsruhe Institute of Technology

Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> im Auftrag von Justin Lemkul
<jalem...@vt.edu>
Gesendet: Mittwoch, 2. September 2015 14:13
An: gmx-us...@gromacs.org
Betreff: Re: [gmx-users] trjconv -pbc nojump

On 9/2/15 7:17 AM, Reisser, Sabine (IPC) wrote:

Thanks for the reply, but I don't want the lipids to jump from one edge of the
box to the other, which they do with this option, even though they remain
complete.

Making molecules whole should be the first step, followed by removing jumps.

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

-Justin

Cheers
Sabine

--
Dr. Sabine Reißer
Theoretical Chemical Biology
Institute of Physical Chemistry
Karlsruhe Institute of Technology

Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> im Auftrag von Ganesh Shahane
<ganesh7shah...@gmail.com>
Gesendet: Mittwoch, 2. September 2015 12:19
An: gmx-us...@gromacs.org
Betreff: Re: [gmx-users] trjconv -pbc nojump

Hi Reisser,

Instead of using -pbc nojump, use -pbc whole.

On Wed, Sep 2, 2015 at 2:47 PM, Reisser, Sabine (IPC) <
sabine.reis...@kit.edu> wrote:

Hi,

I want to use trjconv -pbc nojump to create a trajectory without box
jumping of molecules. The molecules (lipids) also start to diffuse out of
the box like they should, but in some a part of the molecule still jumps
(as I could observe in xy direction), while the rest doesn't, leading to
artificially long bonds in VMD. I tried trjconv -pbc nojump both with a tpr
file in the -s option, or a gro file (with only complete molecules), same
result.

I'd be glad if somebody could give me a hint.

Cheers

Sabine

--
Dr. Sabine Reißer
Theoretical Chemical Biology
Institute of Physical Chemistry
Karlsruhe Institute of Technology

--
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--
==

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

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

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

==
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--
==

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

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

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

==
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Re: [gmx-users] trjconv -pbc nojump

2015-09-02 Thread Justin Lemkul

On 9/2/15 7:17 AM, Reisser, Sabine (IPC) wrote:

Thanks for the reply, but I don't want the lipids to jump from one edge of the
box to the other, which they do with this option, even though they remain
complete.

Making molecules whole should be the first step, followed by removing jumps.

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

-Justin

Cheers
Sabine

--
Dr. Sabine Reißer
Theoretical Chemical Biology
Institute of Physical Chemistry
Karlsruhe Institute of Technology

Hi Reisser,

Instead of using -pbc nojump, use -pbc whole.

On Wed, Sep 2, 2015 at 2:47 PM, Reisser, Sabine (IPC) <
sabine.reis...@kit.edu> wrote:

Hi,

I'd be glad if somebody could give me a hint.

Cheers

Sabine

--
Dr. Sabine Reißer
Theoretical Chemical Biology
Institute of Physical Chemistry
Karlsruhe Institute of Technology

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--
==

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

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

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

==
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Re: [gmx-users] trjconv -pbc nojump