Re: [gmx-users] purpose of step pdb files during MD

2017-09-08 Thread Vedat Durmaz 


Am 07.09.2017 um 21:10 schrieb Justin Lemkul:
>
> On 9/7/17 10:29 AM, Vedat Durmaz wrote:
>> i really appreciate this pretty informative answer. and do you also know, 
>> what the infix "n254" or "n2" stands for?
> Node ID.
>
>> what i found strange is that the error occurs after nearly 10M MD steps. in 
>> other copies of the same system, the error doesn't occur at all even after 
>> the entire predefines time span (40ns).
>>
>> it's a long fibril chain (>200 repeating units) of a 7mer polypeptide. the 
>> walls of the triclinic simulation box of size 10x8x70 nm have an initial 
>> distance of 1.5 nm to the fibril and i have chosen "comm-mode  = linear" in 
>> order to keep the system centered. i'm actually wondering, whether that 
>> might have caused the error or whether the system will for sure crash if the 
>> long chain changes its shape to some spheric one that doesn't fit the slim 
>> box anymore.
>>
>> do you have any experience with that?
> Nope, sorry.  A crash after a long simulation time is very unusual and 
> hard to diagnose.  Normally things fail rather quickly.  Does your 
> GROMACS installation pass all regression tests?
>
> -Justin
>

ok. since i haven't compiled this gromacs installation i haven't seen any 
results of its test runs. anyway, i carried out the simulations again and this 
time no error occurred.

thanks again for your help!

vedat


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Re: [gmx-users] purpose of step pdb files during MD

2017-09-07 Thread Justin Lemkul 



On 9/7/17 10:29 AM, Vedat Durmaz wrote:

i really appreciate this pretty informative answer. and do you also know, what the infix 
"n254" or "n2" stands for?


Node ID.


what i found strange is that the error occurs after nearly 10M MD steps. in 
other copies of the same system, the error doesn't occur at all even after the 
entire predefines time span (40ns).

it's a long fibril chain (>200 repeating units) of a 7mer polypeptide. the walls of the 
triclinic simulation box of size 10x8x70 nm have an initial distance of 1.5 nm to the fibril 
and i have chosen "comm-mode  = linear" in order to keep the system centered. i'm 
actually wondering, whether that might have caused the error or whether the system will for 
sure crash if the long chain changes its shape to some spheric one that doesn't fit the slim 
box anymore.

do you have any experience with that?


Nope, sorry.  A crash after a long simulation time is very unusual and 
hard to diagnose.  Normally things fail rather quickly.  Does your 
GROMACS installation pass all regression tests?


-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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Re: [gmx-users] purpose of step pdb files during MD

2017-09-07 Thread Vedat Durmaz 

i really appreciate this pretty informative answer. and do you also know, what 
the infix "n254" or "n2" stands for?

what i found strange is that the error occurs after nearly 10M MD steps. in 
other copies of the same system, the error doesn't occur at all even after the 
entire predefines time span (40ns).

it's a long fibril chain (>200 repeating units) of a 7mer polypeptide. the 
walls of the triclinic simulation box of size 10x8x70 nm have an initial 
distance of 1.5 nm to the fibril and i have chosen "comm-mode  = linear" in 
order to keep the system centered. i'm actually wondering, whether that might 
have caused the error or whether the system will for sure crash if the long 
chain changes its shape to some spheric one that doesn't fit the slim box 
anymore.

do you have any experience with that?

vedat



Am 07.09.2017 um 14:26 schrieb Justin Lemkul:
>
> On 9/6/17 5:55 AM, Vedat Durmaz wrote:
>> hi guys,
>>
>> from time to time i'm faced with GMX output files during MD called, e.g. in 
>> the current case:
>>
>> step8164372b_n254.pdb
>> step8164372b_n2.pdb
>> step8164372c_n254.pdb
>> step8164372c_n2.pdb
>>
>> what i know is that they are related to kind of exploding systems. however, 
>> i'm not really able to interpret their content. if i visualize them in VMD, 
>> i see a subset of my system surounded by explicit water molecules where the 
>> two *n254* files contain a larger part of my fibrils (polypeptides) than the 
>> *n2* files which only show few atoms of one particular amino acid. but if i 
>> pick certain atoms of the amino acids, they are often not correctly assigned 
>> to residue names and the atom index shown in VMD is different from the index 
>> listed in the underlying gro file.
>>
>> where can i find detailed information about how to interpret the names and 
>> contents of these files? why are exactly these atoms written to the pdb 
>> files and what does the file name tell me?
> These files contain the atoms in a given domain (e.g. on a certain CPU 
> core) and are before (b) and after (c) applying constraints of a given 
> step.  I personally have never found them to be useful in determining 
> anything, but they are an indicator of physical instability.
>
> -Justin
>


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Re: [gmx-users] purpose of step pdb files during MD

2017-09-07 Thread Justin Lemkul 



On 9/6/17 5:55 AM, Vedat Durmaz wrote:

hi guys,

from time to time i'm faced with GMX output files during MD called, e.g. in the 
current case:

step8164372b_n254.pdb
step8164372b_n2.pdb
step8164372c_n254.pdb
step8164372c_n2.pdb

what i know is that they are related to kind of exploding systems. however, i'm 
not really able to interpret their content. if i visualize them in VMD, i see a 
subset of my system surounded by explicit water molecules where the two *n254* 
files contain a larger part of my fibrils (polypeptides) than the *n2* files 
which only show few atoms of one particular amino acid. but if i pick certain 
atoms of the amino acids, they are often not correctly assigned to residue 
names and the atom index shown in VMD is different from the index listed in the 
underlying gro file.

where can i find detailed information about how to interpret the names and 
contents of these files? why are exactly these atoms written to the pdb files 
and what does the file name tell me?


These files contain the atoms in a given domain (e.g. on a certain CPU 
core) and are before (b) and after (c) applying constraints of a given 
step.  I personally have never found them to be useful in determining 
anything, but they are an indicator of physical instability.


-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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Re: [gmx-users] purpose of step pdb files during MD

2017-09-07 Thread Vytautas Rakeviius 
Energy minimization output explains them. I do not think they are important if 
you get good energy minimization after all.
 

On Thursday, September 7, 2017, 3:41:59 AM GMT+3, Vedat Durmaz 
 wrote:  
 
 
hi guys,

from time to time i'm faced with GMX output files during MD called, e.g. in the 
current case:

step8164372b_n254.pdb
step8164372b_n2.pdb
step8164372c_n254.pdb
step8164372c_n2.pdb

what i know is that they are related to kind of exploding systems. however, i'm 
not really able to interpret their content. if i visualize them in VMD, i see a 
subset of my system surounded by explicit water molecules where the two *n254* 
files contain a larger part of my fibrils (polypeptides) than the *n2* files 
which only show few atoms of one particular amino acid. but if i pick certain 
atoms of the amino acids, they are often not correctly assigned to residue 
names and the atom index shown in VMD is different from the index listed in the 
underlying gro file.

where can i find detailed information about how to interpret the names and 
contents of these files? why are exactly these atoms written to the pdb files 
and what does the file name tell me?

any hint is appreciated.

many thanks,

vedat durmaz


-- 
Vedat Durmaz
Computational Molecular Design
Zuse Institute Berlin (ZIB)
Takustrasse 7
14195 Berlin, Germany
T: +49-30-84185-139
F: +49-30-84185-107
http://www.zib.de/durmaz

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[gmx-users] purpose of step pdb files during MD

2017-09-06 Thread Vedat Durmaz 

hi guys,

from time to time i'm faced with GMX output files during MD called, e.g. in the 
current case:

step8164372b_n254.pdb
step8164372b_n2.pdb
step8164372c_n254.pdb
step8164372c_n2.pdb

what i know is that they are related to kind of exploding systems. however, i'm 
not really able to interpret their content. if i visualize them in VMD, i see a 
subset of my system surounded by explicit water molecules where the two *n254* 
files contain a larger part of my fibrils (polypeptides) than the *n2* files 
which only show few atoms of one particular amino acid. but if i pick certain 
atoms of the amino acids, they are often not correctly assigned to residue 
names and the atom index shown in VMD is different from the index listed in the 
underlying gro file.

where can i find detailed information about how to interpret the names and 
contents of these files? why are exactly these atoms written to the pdb files 
and what does the file name tell me?

any hint is appreciated.

many thanks,

vedat durmaz


-- 
Vedat Durmaz
Computational Molecular Design
Zuse Institute Berlin (ZIB)
Takustrasse 7
14195 Berlin, Germany
T: +49-30-84185-139
F: +49-30-84185-107
http://www.zib.de/durmaz


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