Re: [gmx-users] g_wham gets stuck

[Jochen Hub]

Amir Marcovitz wrote:

Thank you Jochem,
 
In your last reply, did you mean that i can perform the WHAM on 
Various histograms that were collected with different force constants? 
i mean , will it know to do the correction for the biasing potential
Yes, WHAM does not require identical force constants. Just make sure 
that the order of tpr and pullx files agree in the -it and -ix input agree.


Jochen




amir
On Fri, Apr 30, 2010 at 4:00 PM, Jochen Hub > wrote:


Justin A. Lemkul wrote:



Amir Marcovitz wrote:

Thanks for your answers,

I tried to struggle a bit more with that today.
my input dat files listings (i.e., tpr-files.dat,
pullf-files.dat and pullx-files.dat) are fine and
consistent with other in terms of file numbering.
i use gromacs 4.0.5 on Linux with gcc 4.1.2 compiler.


Time and time again, we have to point out the bold warning on
the Downloads page:

"WARNING: do not use the gcc 4.1.x set of compilers. They are
broken. These compilers come with recent Linux distrubutions
like Fedora 5/6 etc."

Buggy behavior that is difficult to diagnose is often due to
these faulty compilers.


i run: *g_wham -it tpr-files.dat -if pullf-files.dat -o
-hist -unit kCal -b 1000*(my data is 16ns long and i
ignore the first ns)

and it starts reporting that the file are read:

Reading file topol742.tpr, VERSION 4.0.5 (single precision)
File topol742.tpr, 1 groups, geometry "distance",
dimensions [N Y N], (1 dimensions)
   grp 0) k = 1000.000  inittial distance = 2.41331
Reading file topol748.tpr, VERSION 4.0.5 (single precision)
Reading file topol761.tpr, VERSION 4.0.5 (single precision)
Reading file topol792.tpr, VERSION 4.0.5 (single precision)
and so on..

it reports that the boundaries are found and continue to
read until it stucks..

However, when i do the WHAM with the pullx files (i.e.,
-ix pullx-files instead of -if pullf-files.dat) the wham
converges within a reasonable time to a PMF profile which
not so smooth.

i therefore have some questions:
1) what is the difference in the profiles for using  pullx
or pullf files?


In principle, there probably shouldn't be any, but if there is
perhaps someone else has seen that.

It should not make any difference at all. It it does, there is
something wrong with the data or g_wham is buggy. With the pullf
files, g_wham simply computes the pullx values from the force and
the force constant. This is not really required since it is more
natural to just work with the pullx, but I added to for the case
that someone forgot to write the pullx and only has the pullf files.



2) suppose that my histograms overlap is poor for some
locations along the pulling vector, how one can solve that?


Better sampling (more time) within the sampling windows, or
more closely-spaced windows.

And maybe stronger force constants. g_wham can combine the runs
with smaller and larger force constants, that is no problem.

That is probably the reason for the weired PMF!

Jochen



3) To generate the input configurations -  what is the
ideal pulling procedure?  ( i used pull =
constant_force, with a small value of K1)


There isn't one "best" method, per se.  The only criterion is
that you have generated configurations from which you can
derive reasonably-spaced windows in which you do sufficient
sampling.

-Justin


Again, Thanks a lot for the quick reply
Amir

On Thu, Apr 29, 2010 at 10:33 AM, Jochen Hub
mailto:joc...@xray.bmc.uu.se>
>> wrote:

   Amir Marcovitz wrote:

   Hi All,

   I have some problems with g_wham, and i already
gone through all
   the postings and didn't find a hint..

   basically, I'm trying to calculate PMF between two
charged
   plates. I've performed a pulling simulation between
the 2 plates
   according to Justin's UMBRELLA tutorial in the
website (all
   steps, i.e., minimization, equilibration etc. up to
that point
   work fine)
   from the pulling i generated input configurations
for the
   umbrella sampling runs (pull=umbrella , rate=0.0),
which are 15
   ns long

Re: [gmx-users] Help for running gromacs

[Krzysztof Mlynarczyk]

Please post more details including the following:

   - What is the exact command line?
   - What group do you select as a "continuous solvent"? I know it might
   sound weird to ask this but what I learned while teaching students is that
   these questions really should be asked when there are problems.
   - Which version of Gromacs are you using?


2010/5/3 priyanka panwar 

> I am  using Gromacs for Simulation of Insulin.I have generated most of the
> files but unable to generate the ions.pdb file.The system is becoming idle
> after the Selection command. A line on the command prompt appears as
> "replacing solvent molecule with Na" and remains as such for many hours. Is
> this step really takes too much time or I am doing something wrong.
> Thanks
> --
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> Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] Help for running gromacs

[priyanka panwar]

Hi,
Thanks for help.
-Command line was:
Number of (3-Atomic) solvent molecules:4256
Replacing solvent molecule 499 (atom 2784) with Na
-Group selected was: 12 (SOL)
-Gromacs version I am using is 3.3.1

On Mon, May 3, 2010 at 4:31 PM, Krzysztof Mlynarczyk
wrote:

> Please post more details including the following:
>
>- What is the exact command line?
>- What group do you select as a "continuous solvent"? I know it might
>sound weird to ask this but what I learned while teaching students is that
>these questions really should be asked when there are problems.
>- Which version of Gromacs are you using?
>
>
> 2010/5/3 priyanka panwar 
>
>> I am  using Gromacs for Simulation of Insulin.I have generated most of the
>> files but unable to generate the ions.pdb file.The system is becoming idle
>> after the Selection command. A line on the command prompt appears as
>> "replacing solvent molecule with Na" and remains as such for many hours. Is
>> this step really takes too much time or I am doing something wrong.
>> Thanks
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
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>>
>
>
> --
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Re: [gmx-users] Help for running gromacs

[Justin A. Lemkul]

priyanka panwar wrote:

Hi,
Thanks for help.
-Command line was:
Number of (3-Atomic) solvent molecules:4256
Replacing solvent molecule 499 (atom 2784) with Na


That's not a command line.  What command did you actually type (exactly) to run 
genion?



-Group selected was: 12 (SOL)
-Gromacs version I am using is 3.3.1



In the absence of any compelling reason (i.e., consistency with previous 
simulations), using a Gromacs version that is four years old is not recommended. 
 The new 4.0.x series is substantially faster and has many new features.


-Justin

On Mon, May 3, 2010 at 4:31 PM, Krzysztof Mlynarczyk 
mailto:mitomas...@gmail.com>> wrote:


Please post more details including the following:

* What is the exact command line?
* What group do you select as a "continuous solvent"? I know it
  might sound weird to ask this but what I learned while
  teaching students is that these questions really should be
  asked when there are problems.
* Which version of Gromacs are you using?


2010/5/3 priyanka panwar mailto:priyankapanwa...@gmail.com>>

I am  using Gromacs for Simulation of Insulin.I have generated
most of the files but unable to generate the ions.pdb file.The
system is becoming idle after the Selection command. A line on
the command prompt appears as "replacing solvent molecule with
Na" and remains as such for many hours. Is this step really
takes too much time or I am doing something wrong. 
Thanks

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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Help for running gromacs

[priyanka panwar]

Command line was " genion -s em.tpr -o ions.pdb -np 4"

On Mon, May 3, 2010 at 5:19 PM, Justin A. Lemkul  wrote:

>
>
> priyanka panwar wrote:
>
>> Hi,
>> Thanks for help.
>> -Command line was:
>> Number of (3-Atomic) solvent molecules:4256
>> Replacing solvent molecule 499 (atom 2784) with Na
>>
>
> That's not a command line.  What command did you actually type (exactly) to
> run genion?
>
>
>  -Group selected was: 12 (SOL)
>> -Gromacs version I am using is 3.3.1
>>
>>
> In the absence of any compelling reason (i.e., consistency with previous
> simulations), using a Gromacs version that is four years old is not
> recommended.  The new 4.0.x series is substantially faster and has many new
> features.
>
> -Justin
>
>  On Mon, May 3, 2010 at 4:31 PM, Krzysztof Mlynarczyk <
>> mitomas...@gmail.com > wrote:
>>
>>Please post more details including the following:
>>
>>* What is the exact command line?
>>* What group do you select as a "continuous solvent"? I know it
>>  might sound weird to ask this but what I learned while
>>  teaching students is that these questions really should be
>>  asked when there are problems.
>>* Which version of Gromacs are you using?
>>
>>
>>2010/5/3 priyanka panwar >>
>>
>>
>>I am  using Gromacs for Simulation of Insulin.I have generated
>>most of the files but unable to generate the ions.pdb file.The
>>system is becoming idle after the Selection command. A line on
>>the command prompt appears as "replacing solvent molecule with
>>Na" and remains as such for many hours. Is this step really
>>takes too much time or I am doing something wrong. Thanks
>>--
>>gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search
>>before posting!
>>Please don't post (un)subscribe requests to the list. Use the
>>www interface or send it to gmx-users-requ...@gromacs.org
>>.
>>
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>--
>>gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before
>>posting!
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>>.
>>
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>>
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
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Re: [gmx-users] Help for running gromacs

[shayamra]

Hi,
No need to include "-np 4" at all. genion command does not take  
advantage of multiple processors (nor does it need to).


Try rerunning the command without -np 4.

-Shay

Quoting "priyanka panwar" :


Command line was " genion -s em.tpr -o ions.pdb -np 4"

On Mon, May 3, 2010 at 5:19 PM, Justin A. Lemkul  wrote:




priyanka panwar wrote:


Hi,
Thanks for help.
-Command line was:
Number of (3-Atomic) solvent molecules:4256
Replacing solvent molecule 499 (atom 2784) with Na



That's not a command line.  What command did you actually type (exactly) to
run genion?


 -Group selected was: 12 (SOL)

-Gromacs version I am using is 3.3.1



In the absence of any compelling reason (i.e., consistency with previous
simulations), using a Gromacs version that is four years old is not
recommended.  The new 4.0.x series is substantially faster and has many new
features.

-Justin

 On Mon, May 3, 2010 at 4:31 PM, Krzysztof Mlynarczyk <

mitomas...@gmail.com > wrote:

   Please post more details including the following:

   * What is the exact command line?
   * What group do you select as a "continuous solvent"? I know it
 might sound weird to ask this but what I learned while
 teaching students is that these questions really should be
 asked when there are problems.
   * Which version of Gromacs are you using?


   2010/5/3 priyanka panwar mailto:priyankapanwa...@gmail.com>>


   I am  using Gromacs for Simulation of Insulin.I have generated
   most of the files but unable to generate the ions.pdb file.The
   system is becoming idle after the Selection command. A line on
   the command prompt appears as "replacing solvent molecule with
   Na" and remains as such for many hours. Is this step really
   takes too much time or I am doing something wrong. Thanks
   --
   gmx-users mailing listgmx-users@gromacs.org
   

   http://lists.gromacs.org/mailman/listinfo/gmx-users
   Please search the archive at http://www.gromacs.org/search
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Help for running gromacs

[priyanka panwar]

Hi,
I tried it that way also, but in that case it displays a message "No ions to
add and no potential to generate" and it is also not generating ions.pdb
file but it is creating genion.log file.

On Mon, May 3, 2010 at 6:02 PM,  wrote:

> Hi,
> No need to include "-np 4" at all. genion command does not take advantage
> of multiple processors (nor does it need to).
>
> Try rerunning the command without -np 4.
>
> -Shay
>
>
> Quoting "priyanka panwar" :
>
>  Command line was " genion -s em.tpr -o ions.pdb -np 4"
>>
>> On Mon, May 3, 2010 at 5:19 PM, Justin A. Lemkul  wrote:
>>
>>
>>>
>>> priyanka panwar wrote:
>>>
>>>  Hi,
 Thanks for help.
 -Command line was:
 Number of (3-Atomic) solvent molecules:4256
 Replacing solvent molecule 499 (atom 2784) with Na


>>> That's not a command line.  What command did you actually type (exactly)
>>> to
>>> run genion?
>>>
>>>
>>>  -Group selected was: 12 (SOL)
>>>
 -Gromacs version I am using is 3.3.1


  In the absence of any compelling reason (i.e., consistency with
>>> previous
>>> simulations), using a Gromacs version that is four years old is not
>>> recommended.  The new 4.0.x series is substantially faster and has many
>>> new
>>> features.
>>>
>>> -Justin
>>>
>>>  On Mon, May 3, 2010 at 4:31 PM, Krzysztof Mlynarczyk <
>>>
 mitomas...@gmail.com > wrote:

   Please post more details including the following:

   * What is the exact command line?
   * What group do you select as a "continuous solvent"? I know it
 might sound weird to ask this but what I learned while
 teaching students is that these questions really should be
 asked when there are problems.
   * Which version of Gromacs are you using?


   2010/5/3 priyanka panwar >>>   >


   I am  using Gromacs for Simulation of Insulin.I have generated
   most of the files but unable to generate the ions.pdb file.The
   system is becoming idle after the Selection command. A line on
   the command prompt appears as "replacing solvent molecule with
   Na" and remains as such for many hours. Is this step really
   takes too much time or I am doing something wrong. Thanks
   --
   gmx-users mailing listgmx-users@gromacs.org
   

   http://lists.gromacs.org/mailman/listinfo/gmx-users
   Please search the archive at http://www.gromacs.org/search
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  --
>>> 
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> 
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
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>>> interface
>>> or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>>
>>
>
> --
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Re: [gmx-users] Help for running gromacs

[Erik Marklund]

-np is not about number of processors in the case of genion. It's the 
number of positive ions to insert.


shaya...@post.tau.ac.il skrev:

Hi,
No need to include "-np 4" at all. genion command does not take 
advantage of multiple processors (nor does it need to).


Try rerunning the command without -np 4.

-Shay

Quoting "priyanka panwar" :


Command line was " genion -s em.tpr -o ions.pdb -np 4"

On Mon, May 3, 2010 at 5:19 PM, Justin A. Lemkul  
wrote:





priyanka panwar wrote:


Hi,
Thanks for help.
-Command line was:
Number of (3-Atomic) solvent molecules:4256
Replacing solvent molecule 499 (atom 2784) with Na



That's not a command line.  What command did you actually type 
(exactly) to

run genion?


 -Group selected was: 12 (SOL)

-Gromacs version I am using is 3.3.1


In the absence of any compelling reason (i.e., consistency with 
previous

simulations), using a Gromacs version that is four years old is not
recommended.  The new 4.0.x series is substantially faster and has 
many new

features.

-Justin

 On Mon, May 3, 2010 at 4:31 PM, Krzysztof Mlynarczyk <

mitomas...@gmail.com > wrote:

   Please post more details including the following:

   * What is the exact command line?
   * What group do you select as a "continuous solvent"? I know it
 might sound weird to ask this but what I learned while
 teaching students is that these questions really should be
 asked when there are problems.
   * Which version of Gromacs are you using?


   2010/5/3 priyanka panwar mailto:priyankapanwa...@gmail.com>>


   I am  using Gromacs for Simulation of Insulin.I have generated
   most of the files but unable to generate the ions.pdb file.The
   system is becoming idle after the Selection command. A line on
   the command prompt appears as "replacing solvent molecule with
   Na" and remains as such for many hours. Is this step really
   takes too much time or I am doing something wrong. 
Thanks

   --
   gmx-users mailing listgmx-users@gromacs.org
   

   http://lists.gromacs.org/mailman/listinfo/gmx-users
   Please search the archive at http://www.gromacs.org/search
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Re: [gmx-users] Help for running gromacs

[Justin A. Lemkul]

What compilers did you use to install Gromacs?  Often times hangs and other 
memory errors are related to buggy compilers.


-Justin

priyanka panwar wrote:

Command line was " genion -s em.tpr -o ions.pdb -np 4"

On Mon, May 3, 2010 at 5:19 PM, Justin A. Lemkul > wrote:




priyanka panwar wrote:

Hi,
Thanks for help.
-Command line was:
Number of (3-Atomic) solvent molecules:4256
Replacing solvent molecule 499 (atom 2784) with Na


That's not a command line.  What command did you actually type
(exactly) to run genion?


-Group selected was: 12 (SOL)
-Gromacs version I am using is 3.3.1


In the absence of any compelling reason (i.e., consistency with
previous simulations), using a Gromacs version that is four years
old is not recommended.  The new 4.0.x series is substantially
faster and has many new features.

-Justin

On Mon, May 3, 2010 at 4:31 PM, Krzysztof Mlynarczyk
mailto:mitomas...@gmail.com>
>> wrote:

   Please post more details including the following:

   * What is the exact command line?
   * What group do you select as a "continuous solvent"? I
know it
 might sound weird to ask this but what I learned while
 teaching students is that these questions really should be
 asked when there are problems.
   * Which version of Gromacs are you using?


   2010/5/3 priyanka panwar mailto:priyankapanwa...@gmail.com>
   >>


   I am  using Gromacs for Simulation of Insulin.I have
generated
   most of the files but unable to generate the ions.pdb
file.The
   system is becoming idle after the Selection command. A
line on
   the command prompt appears as "replacing solvent molecule
with
   Na" and remains as such for many hours. Is this step really
   takes too much time or I am doing something wrong.  
  Thanks

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-- 



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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Please

Re: [gmx-users] Help for running gromacs

[priyanka panwar]

I will download latest version of gromacs and start working with it.I will
be back if any face any problem. Thanks to all

On Mon, May 3, 2010 at 6:39 PM, Justin A. Lemkul  wrote:

>
> What compilers did you use to install Gromacs?  Often times hangs and other
> memory errors are related to buggy compilers.
>
> -Justin
>
> priyanka panwar wrote:
>
>> Command line was " genion -s em.tpr -o ions.pdb -np 4"
>>
>> On Mon, May 3, 2010 at 5:19 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>priyanka panwar wrote:
>>
>>Hi,
>>Thanks for help.
>>-Command line was:
>>Number of (3-Atomic) solvent molecules:4256
>>Replacing solvent molecule 499 (atom 2784) with Na
>>
>>
>>That's not a command line.  What command did you actually type
>>(exactly) to run genion?
>>
>>
>>-Group selected was: 12 (SOL)
>>-Gromacs version I am using is 3.3.1
>>
>>
>>In the absence of any compelling reason (i.e., consistency with
>>previous simulations), using a Gromacs version that is four years
>>old is not recommended.  The new 4.0.x series is substantially
>>faster and has many new features.
>>
>>-Justin
>>
>>On Mon, May 3, 2010 at 4:31 PM, Krzysztof Mlynarczyk
>>mailto:mitomas...@gmail.com>
>>>>
>> wrote:
>>
>>   Please post more details including the following:
>>
>>   * What is the exact command line?
>>   * What group do you select as a "continuous solvent"? I
>>know it
>> might sound weird to ask this but what I learned while
>> teaching students is that these questions really should be
>> asked when there are problems.
>>   * Which version of Gromacs are you using?
>>
>>
>>   2010/5/3 priyanka panwar >
>>   >
>>>>
>>
>>
>>   I am  using Gromacs for Simulation of Insulin.I have
>>generated
>>   most of the files but unable to generate the ions.pdb
>>file.The
>>   system is becoming idle after the Selection command. A
>>line on
>>   the command prompt appears as "replacing solvent molecule
>>with
>>   Na" and remains as such for many hours. Is this step really
>>   takes too much time or I am doing something wrong.
>>  Thanks
>>   --
>>   gmx-users mailing listgmx-users@gromacs.org
>>
>>   > >>
>>
>>
>>   http://lists.gromacs.org/mailman/listinfo/gmx-users
>>   Please search the archive at http://www.gromacs.org/search
>>   before posting!
>>   Please don't post (un)subscribe requests to the list. Use
>> the
>>   www interface or send it to gmx-users-requ...@gromacs.org
>>
>>   >>.
>>
>>   Can't post? Read
>>http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>   --
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>>
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>>
>>
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>>
>>   >>.
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>>
>>
>>
>>-- 
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu  | (540) 231-9080
>>
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>>-- gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] cgnr in top file

[leila karami]

Hi all

how cgnr is determind in *.top file? based on?

Any help will highly appreciated!
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Re: [gmx-users] cgnr in top file

[Erik Marklund]

leila karami skrev:

Hi all
 
how cgnr is determind in *.top file? based on?
 
Any help will highly appreciated!
 
Depends on the force field. Generally, they're set according to the 
chargegroups in the original force field, if the force field was 
parameterized with charge groups, that is.


--
---
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Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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Re: [gmx-users] cgnr in top file

[Erik Marklund]

Erik Marklund skrev:

leila karami skrev:

Hi all
 
how cgnr is determind in *.top file? based on?
 
Any help will highly appreciated!
 
Depends on the force field. Generally, they're set according to the 
chargegroups in the original force field, if the force field was 
parameterized with charge groups, that is.



...and gromacs uses the information in the rtp file to do that grouping.

--
---
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Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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[gmx-users] cgnr in top file

[leila karami]

Dear Erik

thank for your answer.

my rtp file for amber 03 force field is as follow :

[ NGLY ]
 [ atoms ]
 Namber99_39   0.29430 1
H1amber99_17   0.16420 2
H2amber99_17   0.16420 3
H3amber99_17   0.16420 4
CAamber99_11  -0.01000 5
   HA1amber99_28   0.08950 6
   HA2amber99_28   0.08950 7
 Camber99_20.61630 8
 Oamber99_41  -0.57220 9

and my top file is as follow :

[ atoms
]
;   nr   type  resnr residue  atom   cgnr charge   mass
 1 amber99_39  1   NGLY  N  1 0.2943  14.01
 2 amber99_17  1   NGLY H1  2 0.1642  1.008
 3 amber99_17  1   NGLY H2  2 0.1642  1.008
 4 amber99_17  1   NGLY H3  2 0.1642  1.008
 5 amber99_11  1   NGLY CA  3  -0.01  12.01
 6 amber99_28  1   NGLYHA1  4 0.0895  1.008
 7 amber99_28  1   NGLYHA2  5 0.0895  1.008
 8  amber99_2  1   NGLY  C6 0.6163  12.01
 9 amber99_41  1   NGLY  O   7-0.5722 16

what relation is there between both of my rtp and top file in above ?
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Re: [gmx-users] cgnr in top file

[Erik Marklund]

The last column in your rtp entry holds the chargegroup numbers. The 
cgnr column in your top file looks just like it. Amber03 was not 
parameterized with charge groups, so the atoms are not groupt together 
as you can see.


Erik

leila karami skrev:

Dear Erik
 
thank for your answer.
 
my rtp file for amber 03 force field is as follow :
 
[ NGLY ]
 [ atoms ]  
 Namber99_39   0.29430 1

H1amber99_17   0.16420 2
H2amber99_17   0.16420 3
H3amber99_17   0.16420 4
CAamber99_11  -0.01000 5
   HA1amber99_28   0.08950 6
   HA2amber99_28   0.08950 7
 Camber99_20.61630 8
 Oamber99_41  -0.57220 9
 
and my top file is as follow :
 
[ atoms 
] 
;   nr   type  resnr residue  atom   cgnr charge   mass  
 1 amber99_39  1   NGLY  N  1 0.2943  14.01  
 2 amber99_17  1   NGLY H1  2 0.1642  1.008  
 3 amber99_17  1   NGLY H2  2 0.1642  1.008  
 4 amber99_17  1   NGLY H3  2 0.1642  1.008   
 5 amber99_11  1   NGLY CA  3  -0.01  12.01   
 6 amber99_28  1   NGLYHA1  4 0.0895  1.008   
 7 amber99_28  1   NGLYHA2  5 0.0895  1.008   
 8  amber99_2  1   NGLY  C6 0.6163  12.01  
 9 amber99_41  1   NGLY  O   7-0.5722 16  
 
what relation is there between both of my rtp and top file in above ?



--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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Re: [gmx-users] cgnr in top file

[Justin A. Lemkul]

leila karami wrote:

Dear Erik
 
thank for your answer.
 
my rtp file for amber 03 force field is as follow :
 
[ NGLY ]
 [ atoms ]  
 Namber99_39   0.29430 1

H1amber99_17   0.16420 2
H2amber99_17   0.16420 3
H3amber99_17   0.16420 4
CAamber99_11  -0.01000 5
   HA1amber99_28   0.08950 6
   HA2amber99_28   0.08950 7
 Camber99_20.61630 8
 Oamber99_41  -0.57220 9
 
and my top file is as follow :
 
[ atoms 
] 
;   nr   type  resnr residue  atom   cgnr charge   mass  
 1 amber99_39  1   NGLY  N  1 0.2943  14.01  
 2 amber99_17  1   NGLY H1  2 0.1642  1.008  
 3 amber99_17  1   NGLY H2  2 0.1642  1.008  
 4 amber99_17  1   NGLY H3  2 0.1642  1.008   
 5 amber99_11  1   NGLY CA  3  -0.01  12.01   
 6 amber99_28  1   NGLYHA1  4 0.0895  1.008   
 7 amber99_28  1   NGLYHA2  5 0.0895  1.008   
 8  amber99_2  1   NGLY  C6 0.6163  12.01  
 9 amber99_41  1   NGLY  O   7-0.5722 16  
 
what relation is there between both of my rtp and top file in above ?




When running pdb2gmx, the .rtp file is used to build the topology, assign 
charges and atom types, etc.  It looks like pdb2gmx is creating a single charge 
group for your N-terminal amine instead of placing each atom in individual 
charge groups.  The AMBER parameterization procedure did not use charge groups, 
so each atom is generally considered its own "group" for the purposes of running 
simulations in Gromacs.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] cgnr in top file

[leila karami]

Dear Erik

you said Amber03 was not parameterized with charge groups and last column in
your rtp entry holds the chargegroup numbers. but
cgnr column in my top file does not looks just like it. in case of H1, H2
and H3.

* H1amber99_17   0.16420 2
** H2amber99_17   0.16420 3
** H3amber99_17   0.16420 4
**** *. that's ok. but why

*and my top file is as follow :
**
**
**nr   type  resnr  residue  atom   cgnr   charge mass
**  **2 amber99_17  1   NGLY H1  2 0.1642  1.008
**  3 amber99_17  1   NGLY H2  2 0.1642  1.008
**  4 amber99_17  1   NGLY H3  2 0.1642  1.008
**   *
thanks for your attention
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Re: [gmx-users] cgnr in top file

[Erik Marklund]

True. I guess gromacs groups together the terminal hydrogens, overriding 
the original force field parameters. Can't say why that decision was 
made, but it will influence your simulation very little.


Erik

leila karami skrev:

Dear Erik
 
you said Amber03 was not parameterized with charge groups and last 
column in your rtp entry holds the chargegroup numbers. but
cgnr column in my top file does not looks just like it. in case of H1, 
H2 and H3.
 
/ H1amber99_17   0.16420 2

// H2amber99_17   0.16420 3
// H3amber99_17   0.16420 4
//// /. that's ok. but why
 
/and my top file is as follow :
//  
//
//nr   type  resnr  residue  atom   cgnr   charge 
mass  
//  //2 amber99_17  1   NGLY H1  2 0.1642  1.008  
//  3 amber99_17  1   NGLY H2  2 0.1642  1.008  
//  4 amber99_17  1   NGLY H3  2 0.1642  1.008   
//   /
thanks for your attention



--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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Re: [gmx-users] cgnr in top file

[Justin A. Lemkul]

Erik Marklund wrote:
True. I guess gromacs groups together the terminal hydrogens, overriding 
the original force field parameters. Can't say why that decision was 
made, but it will influence your simulation very little.


I think there was a bug report some time ago involving virtual sites on the 
termini of all-atom force fields causing a crash when the terminus crossed a 
periodic boundary.  Could be related to that, although I can't remember the 
exact progress behind the fix.


-Justin



Erik

leila karami skrev:

Dear Erik
 
you said Amber03 was not parameterized with charge groups and last 
column in your rtp entry holds the chargegroup numbers. but
cgnr column in my top file does not looks just like it. in case of H1, 
H2 and H3.
 
/ H1amber99_17   0.16420 2

// H2amber99_17   0.16420 3
// H3amber99_17   0.16420 4
//// /. that's ok. but why
 
/and my top file is as follow :
//  ////
nr   type  resnr  residue  atom   cgnr   charge mass  
//  //2 amber99_17  1   NGLY H1  2 0.1642  
1.008  //  3 amber99_17  1   NGLY H2  2 
0.1642  1.008  //  4 amber99_17  1   NGLY H3  
2 0.1642  1.008   //   /
thanks for your attention





--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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RE: [gmx-users] cgnr in top file

[Berk Hess]

Hi,

This is not a decision, but a limitation of the grompp code.
I have fixed this in the git release.

Simply editing the charge group numbers by hand to make them all different
should work.

Berk

> Date: Mon, 3 May 2010 10:22:54 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] cgnr in top file
> 
> 
> 
> Erik Marklund wrote:
> > True. I guess gromacs groups together the terminal hydrogens, overriding 
> > the original force field parameters. Can't say why that decision was 
> > made, but it will influence your simulation very little.
> 
> I think there was a bug report some time ago involving virtual sites on the 
> termini of all-atom force fields causing a crash when the terminus crossed a 
> periodic boundary.  Could be related to that, although I can't remember the 
> exact progress behind the fix.
> 
> -Justin
> 
> > 
> > Erik
> > 
> > leila karami skrev:
> >> Dear Erik
> >>  
> >> you said Amber03 was not parameterized with charge groups and last 
> >> column in your rtp entry holds the chargegroup numbers. but
> >> cgnr column in my top file does not looks just like it. in case of H1, 
> >> H2 and H3.
> >>  
> >> / H1amber99_17   0.16420 2
> >> // H2amber99_17   0.16420 3
> >> // H3amber99_17   0.16420 4
> >> //// /. that's ok. but why
> >>  
> >> /and my top file is as follow :
> >> //  ////
> >> nr   type  resnr  residue  atom   cgnr   charge mass  
> >> //  //2 amber99_17  1   NGLY H1  2 0.1642  
> >> 1.008  //  3 amber99_17  1   NGLY H2  2 
> >> 0.1642  1.008  //  4 amber99_17  1   NGLY H3  
> >> 2 0.1642  1.008   //   /
> >> thanks for your attention
> > 
> > 
> 
> -- 
> 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> -- 
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[gmx-users] energy minimization + freeze atoms

[Nilesh Dhumal]

Hello,
I am trying to do energy minimization with  normal mode analysis for my 
ststem.

I used freezegrps and freezedim optitions to freeze the atoms.

I found that after minimization the atoms are moved.

Can you tell me how to freeze atoms for energy minimzation.

I need this geometry for normal mode analysis.


Thanks

Nilesh




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[gmx-users] Unneccessary bonding

[abdullah ahmed]

Hello, 

I am a new user to GROMACS and so this question maybe somewhat naive. 

 My objective is to run a few steps of minimization on a PDB structure and then 
obtain the energy value. To do so I ran the procedure suggested in the tutorial 
called "speptide" using the .mdp file provided in this procedure.   

The structure I am using has two oppositely charged residues facing each other. 
The initial distance(3.2 A°) is such that ionic interactions should occur 
between them, thereby creating a low coloumb energy score after 
minimization/molecular dynamics (check by looking at the log-file). However, a 
covalent bond is being created between them instead. This should not be 
happening. 

Does anyone have any ideas on what may be happening and how I can fix it? 

If this information is not sufficient, please let me know, and thank you in 
advance.

Abdullah Ahmed 
  
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Re: [gmx-users] Unneccessary bonding

[XAvier Periole]

On May 3, 2010, at 5:16 PM, abdullah ahmed wrote:


Hello,

I am a new user to GROMACS and so this question maybe somewhat naive.

My objective is to run a few steps of minimization on a PDB  
structure and then obtain the energy value. To do so I ran the  
procedure suggested in the tutorial called "speptide" using the .mdp  
file provided in this procedure.


The structure I am using has two oppositely charged residues facing  
each other. The initial distance(3.2 A°) is such that ionic  
interactions should occur between them, thereby creating a low  
coloumb energy score after minimization/molecular dynamics (check by  
looking at the log-file). However, a covalent bond is being created  
between them instead. This should not be happening.
What do you mean a covalent bond is being created! This is basically  
not possible!
Would that just be a visualization effect? This could result from the  
fact that the two atoms
get really close to each other and thereby your visualization program  
thinks it is a covalent

bond.


Does anyone have any ideas on what may be happening and how I can  
fix it?


If this information is not sufficient, please let me know, and thank  
you in advance.


Abdullah Ahmed

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RE: [gmx-users] Unneccessary bonding

[abdullah ahmed]

Thank you very much for your reply, 
I agree it is probably a visualization of the effect, and that there is no 
bond. However, the distance between the two atoms participating in this 
"phantom bond" is 1.4 A°. Isn't that too close? Shouldn't it be considered a 
clash? 

Abdullah  

From: x.peri...@rug.nl
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Unneccessary bonding
Date: Mon, 3 May 2010 17:36:29 +0200


On May 3, 2010, at 5:16 PM, abdullah ahmed wrote:Hello, 

I am a new user to GROMACS and so this question maybe somewhat naive. 

My objective is to run a few steps of minimization on a PDB structure and then 
obtain the energy value. To do so I ran the procedure suggested in the tutorial 
called "speptide" using the .mdp file provided in this procedure.   

The structure I am using has two oppositely charged residues facing each other. 
The initial distance(3.2 A°) is such that ionic interactions should occur 
between them, thereby creating a low coloumb energy score after 
minimization/molecular dynamics (check by looking at the log-file). However, a 
covalent bond is being created between them instead. This should not be 
happening. 
What do you mean a covalent bond is being created! This is basically not 
possible! Would that just be a visualization effect? This could result from the 
fact that the two atomsget really close to each other and thereby your 
visualization program thinks it is a covalentbond.

Does anyone have any ideas on what may be happening and how I can fix it? 

If this information is not sufficient, please let me know, and thank you in 
advance.

Abdullah Ahmed 

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Re: [gmx-users] Unneccessary bonding

[XAvier Periole]

On May 3, 2010, at 5:52 PM, abdullah ahmed wrote:


Thank you very much for your reply,
I agree it is probably a visualization of the effect, and that there  
is no bond. However, the distance between the two atoms  
participating in this "phantom bond" is 1.4 A°. Isn't that too  
close? Shouldn't it be considered a clash?
1.4 is short for sure! an H-bond goes down to 1.0 ... and charged ions  
make (depending on their size) bonds with

water oxygen around 2.0 ...
If you have two opposite charges in front of each other that might well
be happening!
What kind of atoms are the ones getting close?


Abdullah

From: x.peri...@rug.nl
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Unneccessary bonding
Date: Mon, 3 May 2010 17:36:29 +0200


On May 3, 2010, at 5:16 PM, abdullah ahmed wrote:

Hello,

I am a new user to GROMACS and so this question maybe somewhat naive.

My objective is to run a few steps of minimization on a PDB  
structure and then obtain the energy value. To do so I ran the  
procedure suggested in the tutorial called "speptide" using the .mdp  
file provided in this procedure.


The structure I am using has two oppositely charged residues facing  
each other. The initial distance(3.2 A°) is such that ionic  
interactions should occur between them, thereby creating a low  
coloumb energy score after minimization/molecular dynamics (check by  
looking at the log-file). However, a covalent bond is being created  
between them instead. This should not be happening.
What do you mean a covalent bond is being created! This is basically  
not possible!
Would that just be a visualization effect? This could result from  
the fact that the two atoms
get really close to each other and thereby your visualization  
program thinks it is a covalent

bond.

Does anyone have any ideas on what may be happening and how I can  
fix it?


If this information is not sufficient, please let me know, and thank  
you in advance.


Abdullah Ahmed

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[gmx-users] electrostatic interactions

[abdullah ahmed]

Hello everyone, 

I have just started using GROMACS, and apolise if my question is naive. 

Basically, I'd like to ask if anyone has some suggestions regarding the 
settings I should use for electrostatic interactions? 

I have two protein molecules similar in everyway except, one has a single 
negative charge inside the molecule, and another has two opposite charges 
facing each other. The opposite charges are close enough to form electrostatic 
interactions, so would expect the coloumb energy for this molecule to be less 
than the other after minimization/molecular dynamics. However, the results show 
that they are almost the same. 

Thank you in advance for your help,
Abdullah Ahmed
  
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RE: [gmx-users] Unneccessary bonding

[abdullah ahmed]

Dear Mr. Periole,

The atoms that are getting close are oxygen from a GLU residue and hydrogen 
from a LYS residue. 

Abdullah

From: x.peri...@rug.nl
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Unneccessary bonding
Date: Mon, 3 May 2010 18:00:43 +0200


On May 3, 2010, at 5:52 PM, abdullah ahmed wrote:Thank you very much for your 
reply, 
I agree it is probably a visualization of the effect, and that there is no 
bond. However, the distance between the two atoms participating in this 
"phantom bond" is 1.4 A°. Isn't that too close? Shouldn't it be considered a 
clash? 
1.4 is short for sure! an H-bond goes down to 1.0 ... and charged ions make 
(depending on their size) bonds with water oxygen around 2.0 ... If you have 
two opposite charges in front of each other that might well be happening! What 
kind of atoms are the ones getting close? 

Abdullah  

From: x.peri...@rug.nl
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Unneccessary bonding
Date: Mon, 3 May 2010 17:36:29 +0200


On May 3, 2010, at 5:16 PM, abdullah ahmed wrote:Hello, 

I am a new user to GROMACS and so this question maybe somewhat naive. 

My objective is to run a few steps of minimization on a PDB structure and then 
obtain the energy value. To do so I ran the procedure suggested in the tutorial 
called "speptide" using the .mdp file provided in this procedure.   

The structure I am using has two oppositely charged residues facing each other. 
The initial distance(3.2 A°) is such that ionic interactions should occur 
between them, thereby creating a low coloumb energy score after 
minimization/molecular dynamics (check by looking at the log-file). However, a 
covalent bond is being created between them instead. This should not be 
happening. 
What do you mean a covalent bond is being created! This is basically not 
possible! Would that just be a visualization effect? This could result from the 
fact that the two atomsget really close to each other and thereby your 
visualization program thinks it is a covalentbond.

Does anyone have any ideas on what may be happening and how I can fix it? 

If this information is not sufficient, please let me know, and thank you in 
advance.

Abdullah Ahmed 

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Re: [gmx-users] electrostatic interactions

[Justin A. Lemkul]

abdullah ahmed wrote:

Hello everyone,

I have just started using GROMACS, and apolise if my question is naive.

Basically, I'd like to ask if anyone has some suggestions regarding the 
settings I should use for electrostatic interactions?




Well, you haven't shown us what settings you're using or what force field you're 
using, so it's impossible to make any specific recommendation.  Your cutoffs and 
type of long-range electrostatics method will be largely dictated by the force 
field you've chosen.  The primary literature will tell you a lot.


I have two protein molecules similar in everyway except, one has a 
single negative charge inside the molecule, and another has two opposite 
charges facing each other. The opposite charges are close enough to form 
electrostatic interactions, so would expect the coloumb energy for this 
molecule to be less than the other after minimization/molecular 
dynamics. However, the results show that they are almost the same.




It's hard to comment on the accuracy of these results without a lot more 
information (see above).  Other factors include the local geometry of other 
surrounding residues; if the structures are different (even subtly) you 
certainly can't make any generalizations.


-Justin


Thank you in advance for your help,
Abdullah Ahmed


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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Unneccessary bonding

[Justin A. Lemkul]

abdullah ahmed wrote:

Dear Mr. Periole,

The atoms that are getting close are oxygen from a GLU residue and 
hydrogen from a LYS residue.


I don't see anything wrong with a 1.4-A distance between these atoms.  Why do 
you suspect a problem (besides the non-existent bond)?


-Justin



Abdullah


From: x.peri...@rug.nl
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Unneccessary bonding
Date: Mon, 3 May 2010 18:00:43 +0200


On May 3, 2010, at 5:52 PM, abdullah ahmed wrote:

Thank you very much for your reply, 
I agree it is probably a visualization of the effect, and that there

is no bond. However, the distance between the two atoms
participating in this "phantom bond" is 1.4 A°. Isn't that too
close? Shouldn't it be considered a clash? 

1.4 is short for sure! an H-bond goes down to 1.0 ... and charged ions 
make (depending on their size) bonds with 
water oxygen around 2.0 ... 
If you have two opposite charges in front of each other that might well 
be happening! 
What kind of atoms are the ones getting close? 



Abdullah  



From: x.peri...@rug.nl 
To: gmx-users@gromacs.org 
Subject: Re: [gmx-users] Unneccessary bonding
Date: Mon, 3 May 2010 17:36:29 +0200


On May 3, 2010, at 5:16 PM, abdullah ahmed wrote:

Hello, 


I am a new user to GROMACS and so this question maybe somewhat
naive. 


My objective is to run a few steps of minimization on a PDB
structure and then obtain the energy value. To do so I ran the
procedure suggested in the tutorial called "speptide" using the
.mdp file provided in this procedure.   


The structure I am using has two oppositely charged residues
facing each other. The initial distance(3.2 A°) is such that
ionic interactions should occur between them, thereby creating a
low coloumb energy score after minimization/molecular dynamics
(check by looking at the log-file). However, a covalent bond is
being created between them instead. This should not be happening. 


What do you mean a covalent bond is being created! This is basically
not possible! 
Would that just be a visualization effect? This could result from

the fact that the two atoms
get really close to each other and thereby your visualization
program thinks it is a covalent
bond.


Does anyone have any ideas on what may be happening and how I
can fix it? 


If this information is not sufficient, please let me know, and
thank you in advance.

Abdullah Ahmed 



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now. 




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Unneccessary bonding

[XAvier Periole]

On May 3, 2010, at 6:12 PM, Justin A. Lemkul wrote:




abdullah ahmed wrote:

Dear Mr. Periole,
The atoms that are getting close are oxygen from a GLU residue and  
hydrogen from a LYS residue.


I don't see anything wrong with a 1.4-A distance between these  
atoms.  Why do you suspect a problem (besides the non-existent bond)?
Agreed! This is fine ... the question is why they go from 3.5 to  
1.4 ... are they

embedded in the protein interior? At the surface of the protein 
may be a missing water molecule in between them?


-Justin


Abdullah

From: x.peri...@rug.nl
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Unneccessary bonding
Date: Mon, 3 May 2010 18:00:43 +0200
On May 3, 2010, at 5:52 PM, abdullah ahmed wrote:
   Thank you very much for your reply, I agree it is probably a  
visualization of the effect, and that there

   is no bond. However, the distance between the two atoms
   participating in this "phantom bond" is 1.4 A°. Isn't that too
   close? Shouldn't it be considered a clash? 1.4 is short for  
sure! an H-bond goes down to 1.0 ... and charged ions make  
(depending on their size) bonds with water oxygen around 2.0 ... If  
you have two opposite charges in front of each other that might  
well be happening! What kind of atoms are the ones getting  
close? Abdullah   


   From: x.peri...@rug.nl 
   To: gmx-users@gromacs.org 
   Subject: Re: [gmx-users] Unneccessary bonding
   Date: Mon, 3 May 2010 17:36:29 +0200
   On May 3, 2010, at 5:16 PM, abdullah ahmed wrote:
   Hello, I am a new user to GROMACS and so this  
question maybe somewhat
   naive. My objective is to run a few steps of  
minimization on a PDB

   structure and then obtain the energy value. To do so I ran the
   procedure suggested in the tutorial called "speptide" using  
the
   .mdp file provided in this procedure.   The  
structure I am using has two oppositely charged residues

   facing each other. The initial distance(3.2 A°) is such that
   ionic interactions should occur between them, thereby  
creating a

   low coloumb energy score after minimization/molecular dynamics
   (check by looking at the log-file). However, a covalent bond  
is
   being created between them instead. This should not be  
happening. What do you mean a covalent bond is being created!  
This is basically
   not possible! Would that just be a visualization effect?  
This could result from

   the fact that the two atoms
   get really close to each other and thereby your visualization
   program thinks it is a covalent
   bond.
   Does anyone have any ideas on what may be happening and how I
   can fix it? If this information is not sufficient,  
please let me know, and

   thank you in advance.
   Abdullah Ahmed  


   Hotmail: Free, trusted and rich email service. Get it now.
    --  
gmx-users mailing listgmx-users@gromacs.org

   
   http://lists.gromacs.org/mailman/listinfo/gmx-users
   Please search the archive
   at http://www.gromacs.org/search before posting!
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ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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RE: [gmx-users] Unneccessary bonding

[abdullah ahmed]

They are on the inside of the structure. I don't think it is caused by a water 
molecule, because I ran editconf and genbox again and got the same result. (I 
have assumed that water molecules are added to the structure in a random 
fashion in areas not already occupied by other atoms)

If you like I can send you the structures in PDB form. 

> From: x.peri...@rug.nl
> To: jalem...@vt.edu; gmx-users@gromacs.org
> Subject: Re: [gmx-users] Unneccessary bonding
> Date: Mon, 3 May 2010 18:18:31 +0200
> CC: 
> 
> 
> On May 3, 2010, at 6:12 PM, Justin A. Lemkul wrote:
> 
> >
> >
> > abdullah ahmed wrote:
> >> Dear Mr. Periole,
> >> The atoms that are getting close are oxygen from a GLU residue and  
> >> hydrogen from a LYS residue.
> >
> > I don't see anything wrong with a 1.4-A distance between these  
> > atoms.  Why do you suspect a problem (besides the non-existent bond)?
> Agreed! This is fine ... the question is why they go from 3.5 to  
> 1.4 ... are they
> embedded in the protein interior? At the surface of the protein 
> may be a missing water molecule in between them?
> >
> > -Justin
> >
> >> Abdullah
> >> 
> >> From: x.peri...@rug.nl
> >> To: gmx-users@gromacs.org
> >> Subject: Re: [gmx-users] Unneccessary bonding
> >> Date: Mon, 3 May 2010 18:00:43 +0200
> >> On May 3, 2010, at 5:52 PM, abdullah ahmed wrote:
> >>Thank you very much for your reply, I agree it is probably a  
> >> visualization of the effect, and that there
> >>is no bond. However, the distance between the two atoms
> >>participating in this "phantom bond" is 1.4 A°. Isn't that too
> >>close? Shouldn't it be considered a clash? 1.4 is short for  
> >> sure! an H-bond goes down to 1.0 ... and charged ions make  
> >> (depending on their size) bonds with water oxygen around 2.0 ... If  
> >> you have two opposite charges in front of each other that might  
> >> well be happening! What kind of atoms are the ones getting  
> >> close? Abdullah   
> >> 
> >>From: x.peri...@rug.nl 
> >>To: gmx-users@gromacs.org 
> >>Subject: Re: [gmx-users] Unneccessary bonding
> >>Date: Mon, 3 May 2010 17:36:29 +0200
> >>On May 3, 2010, at 5:16 PM, abdullah ahmed wrote:
> >>Hello, I am a new user to GROMACS and so this  
> >> question maybe somewhat
> >>naive. My objective is to run a few steps of  
> >> minimization on a PDB
> >>structure and then obtain the energy value. To do so I ran the
> >>procedure suggested in the tutorial called "speptide" using  
> >> the
> >>.mdp file provided in this procedure.   The  
> >> structure I am using has two oppositely charged residues
> >>facing each other. The initial distance(3.2 A°) is such that
> >>ionic interactions should occur between them, thereby  
> >> creating a
> >>low coloumb energy score after minimization/molecular dynamics
> >>(check by looking at the log-file). However, a covalent bond  
> >> is
> >>being created between them instead. This should not be  
> >> happening. What do you mean a covalent bond is being created!  
> >> This is basically
> >>not possible! Would that just be a visualization effect?  
> >> This could result from
> >>the fact that the two atoms
> >>get really close to each other and thereby your visualization
> >>program thinks it is a covalent
> >>bond.
> >>Does anyone have any ideas on what may be happening and how I
> >>can fix it? If this information is not sufficient,  
> >> please let me know, and
> >>thank you in advance.
> >>Abdullah Ahmed  
> >> 
> >>Hotmail: Free, trusted and rich email service. Get it now.
> >> --  
> >> gmx-users mailing listgmx-users@gromacs.org
> >>
> >>http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>Please search the archive
> >>at http://www.gromacs.org/search before posting!
> >>Please don't post (un)subscribe requests to the list. Use  
> >> the www interface or send it to gmx-users-requ...@gromacs.org
> >>.
> >>Can't post? Read http://www.gromacs.org/mailing_lists/ 
> >> users.php
> >> 
> >> 
> >>Your E-mail and More On-the-Go. Get Windows Live Hotmail Free.  
> >> Sign
> >>up now.  --  
> >> gmx-users mailing listgmx-users@gromacs.org
> >>
> >>http://lists.gromacs.

Re: [gmx-users] electrostatic interactions

[Justin A. Lemkul]

abdullah ahmed wrote:

Thank you for your reply,

Settings:
I am using the procedure outline by the "speptide" tutorial (i.e. 
pdb2gmx, followed by editconf, genbox, grompp, and mdrun). The ".mdp" 
file I've used is as follows:


;User spoel (236)
;Wed Nov  3 17:12:44 1993
;Input file
;
cpp =  /usr/bin/cpp
define  =  -DPOSRES
constraints =  none
integrator  =  steep
nsteps  =  100
;
;Energy minimizing stuff
;
emtol   =  20
emstep  =  0.01

nstcgsteep  =  10
nstcomm =  1
ns_type =  grid
rlist   =  1
rcoulomb=  1.0
rvdw=  1.0
Tcoupl  =  no
Pcoupl  =  no
gen_vel =  no
coulombtype = PME

Force field: Encad all atom force field, using full sovent charges.

Local geometry is identical with the exception of the second charged 
residue, which is replaced by Leucine in one structure. 



Well, all you've done is a simple, restrained energy minimization, which won't 
tell you much about anything.  I don't see much point in using restraints during 
EM anyway.  Running real, unrestrained MD and obtaining suitable averages for 
energies is the only way to make the conclusions I think you're after.


-Justin





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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Unneccessary bonding

[Justin A. Lemkul]

abdullah ahmed wrote:
They are on the inside of the structure. I don't think it is caused by a 
water molecule, because I ran editconf and genbox again and got the same 
result. (I have assumed that water molecules are added to the structure 
in a random fashion in areas not already occupied by other atoms)


If you like I can send you the structures in PDB form.



If the two residues are in the protein interior, there likely won't be water 
there (nor should there be).  Electrostatic interactions in the core of a 
protein is an interesting topic and there is lots of literature about it, 
including whether or not certain ionization states should exist and whether or 
not they are functionally relevant.


For charged residues in a protein interior, I see no problem whatsoever with 
what you're seeing.


-Justin


 > From: x.peri...@rug.nl
 > To: jalem...@vt.edu; gmx-users@gromacs.org
 > Subject: Re: [gmx-users] Unneccessary bonding
 > Date: Mon, 3 May 2010 18:18:31 +0200
 > CC:
 >
 >
 > On May 3, 2010, at 6:12 PM, Justin A. Lemkul wrote:
 >
 > >
 > >
 > > abdullah ahmed wrote:
 > >> Dear Mr. Periole,
 > >> The atoms that are getting close are oxygen from a GLU residue and
 > >> hydrogen from a LYS residue.
 > >
 > > I don't see anything wrong with a 1.4-A distance between these
 > > atoms. Why do you suspect a problem (besides the non-existent bond)?
 > Agreed! This is fine ... the question is why they go from 3.5 to
 > 1.4 ... are they
 > embedded in the protein interior? At the surface of the protein 
 > may be a missing water molecule in between them?
 > >
 > > -Justin
 > >
 > >> Abdullah
 > >> 


 > >> From: x.peri...@rug.nl
 > >> To: gmx-users@gromacs.org
 > >> Subject: Re: [gmx-users] Unneccessary bonding
 > >> Date: Mon, 3 May 2010 18:00:43 +0200
 > >> On May 3, 2010, at 5:52 PM, abdullah ahmed wrote:
 > >> Thank you very much for your reply, I agree it is probably a
 > >> visualization of the effect, and that there
 > >> is no bond. However, the distance between the two atoms
 > >> participating in this "phantom bond" is 1.4 A°. Isn't that too
 > >> close? Shouldn't it be considered a clash? 1.4 is short for
 > >> sure! an H-bond goes down to 1.0 ... and charged ions make
 > >> (depending on their size) bonds with water oxygen around 2.0 ... If
 > >> you have two opposite charges in front of each other that might
 > >> well be happening! What kind of atoms are the ones getting
 > >> close? Abdullah
 > >> 


 > >> From: x.peri...@rug.nl 
 > >> To: gmx-users@gromacs.org 
 > >> Subject: Re: [gmx-users] Unneccessary bonding
 > >> Date: Mon, 3 May 2010 17:36:29 +0200
 > >> On May 3, 2010, at 5:16 PM, abdullah ahmed wrote:
 > >> Hello, I am a new user to GROMACS and so this
 > >> question maybe somewhat
 > >> naive. My objective is to run a few steps of
 > >> minimization on a PDB
 > >> structure and then obtain the energy value. To do so I ran the
 > >> procedure suggested in the tutorial called "speptide" using
 > >> the
 > >> .mdp file provided in this procedure. The
 > >> structure I am using has two oppositely charged residues
 > >> facing each other. The initial distance(3.2 A°) is such that
 > >> ionic interactions should occur between them, thereby
 > >> creating a
 > >> low coloumb energy score after minimization/molecular dynamics
 > >> (check by looking at the log-file). However, a covalent bond
 > >> is
 > >> being created between them instead. This should not be
 > >> happening. What do you mean a covalent bond is being created!
 > >> This is basically
 > >> not possible! Would that just be a visualization effect?
 > >> This could result from
 > >> the fact that the two atoms
 > >> get really close to each other and thereby your visualization
 > >> program thinks it is a covalent
 > >> bond.
 > >> Does anyone have any ideas on what may be happening and how I
 > >> can fix it? If this information is not sufficient,
 > >> please let me know, and
 > >> thank you in advance.
 > >> Abdullah Ahmed
 > >> 


 > >> Hotmail: Free, trusted and rich email service. Get it now.
 > >>  --
 > >> gmx-users mailing list gmx-users@gromacs.org
 > >> 
 > >> http://lists.gromacs.org/mailman/listinfo/gmx-users
 > >> Please search the archive
 > >> at http://www.gromacs.org/search before posting!
 > >> Please don't post (un)subscribe requests to the list. Use
 > >> the www interface or send it to gmx-users-requ...@gromacs.org
 > >> .
 > >> Can't post? Read http://www.gromacs.org/mailing_lists/
 > >> users.php
 > >>
 > >> 


 > >> Your E-mail and More On-the-Go

RE: [gmx-users] electrostatic interactions

[abdullah ahmed]

Thank you for your reply, 

Settings: 
I am using the procedure
 outline by the "speptide" tutorial (i.e. pdb2gmx, followed by editconf,
 genbox, grompp, and mdrun). The ".mdp" file I've used is as follows: 

;   
 User spoel (236)
;Wed Nov  3 17:12:44 1993
;Input file
;
cpp
 =  /usr/bin/cpp
define  =  -DPOSRES 
constraints
 =  none
integrator  =  steep
nsteps  =  100
;
;   
 Energy minimizing stuff
;
emtol   =  20
emstep 
 =  0.01

nstcgsteep  =  10
nstcomm =  1
ns_type
 =  grid
rlist   =  1
rcoulomb=  1.0
rvdw   
 =  1.0
Tcoupl  =  no
Pcoupl  =  no
gen_vel
 =  no
coulombtype = PME

Force field: Encad all atom 
force field, using full sovent charges.

Local geometry is 
identical with the exception of the second charged residue, which is 
replaced by Leucine in one structure.  

> Date: Mon, 3 May 2010 12:11:12 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] electrostatic interactions
> 
> 
> 
> abdullah ahmed wrote:
> > Hello everyone,
> > 
> > I have just started using GROMACS, and apolise if my question is naive.
> > 
> > Basically, I'd like to ask if anyone has some suggestions regarding the 
> > settings I should use for electrostatic interactions?
> > 
> 
> Well, you haven't shown us what settings you're using or what force field 
> you're 
> using, so it's impossible to make any specific recommendation.  Your cutoffs 
> and 
> type of long-range electrostatics method will be largely dictated by the 
> force 
> field you've chosen.  The primary literature will tell you a lot.
> 
> > I have two protein molecules similar in everyway except, one has a 
> > single negative charge inside the molecule, and another has two opposite 
> > charges facing each other. The opposite charges are close enough to form 
> > electrostatic interactions, so would expect the coloumb energy for this 
> > molecule to be less than the other after minimization/molecular 
> > dynamics. However, the results show that they are almost the same.
> > 
> 
> It's hard to comment on the accuracy of these results without a lot more 
> information (see above).  Other factors include the local geometry of other 
> surrounding residues; if the structures are different (even subtly) you 
> certainly can't make any generalizations.
> 
> -Justin
> 
> > Thank you in advance for your help,
> > Abdullah Ahmed
> > 
> > 
> > Hotmail: Powerful Free email with security by Microsoft. Get it now. 
> > 
> > 
> 
> -- 
> 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
  
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[gmx-users] energy minimization + freeze atoms

[Nilesh Dhumal]

Hello,
I am trying to do energy minimization with  normal mode analysis for my
ststem.

I used freezegrps and freezedim optitions to freeze the atoms.

I found that after minimization the atoms are moved.

Can you tell me how to freeze atoms for energy minimzation.

I need this geometry for normal mode analysis.


Thanks

Nilesh





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Re: [gmx-users] Unneccessary bonding

[XAvier Periole]

On May 3, 2010, at 6:27 PM, abdullah ahmed wrote:

They are on the inside of the structure. I don't think it is caused  
by a water molecule, because I ran editconf and genbox again and got  
the same result. (I have assumed that water molecules are added to  
the structure in a random fashion in areas not already occupied by  
other atoms)
genbox is not necessarily able to place water molecules in small  
confined spaces
in a protein. You should check the pdb structure and see if there is  
not a water molecule
in that "space". Note that this was only a idea ... not necessarily  
your problem.
a better probe of the distance between the two residue side chain  
would be to use
the C of the COO group and the N of the NH3 group. You might observe  
reorientation
the the "satellite atoms" (O and H) while the center of the group is  
actually keeping

a reasonable distance.
Basically all goes in checking what kind of deformation you observe  
during your

minimization, a single distance is not necessarily meaningful.

If you like I can send you the structures in PDB form.

Not necessary


> From: x.peri...@rug.nl
> To: jalem...@vt.edu; gmx-users@gromacs.org
> Subject: Re: [gmx-users] Unneccessary bonding
> Date: Mon, 3 May 2010 18:18:31 +0200
> CC:
>
>
> On May 3, 2010, at 6:12 PM, Justin A. Lemkul wrote:
>
> >
> >
> > abdullah ahmed wrote:
> >> Dear Mr. Periole,
> >> The atoms that are getting close are oxygen from a GLU residue  
and

> >> hydrogen from a LYS residue.
> >
> > I don't see anything wrong with a 1.4-A distance between these
> > atoms. Why do you suspect a problem (besides the non-existent  
bond)?

> Agreed! This is fine ... the question is why they go from 3.5 to
> 1.4 ... are they
> embedded in the protein interior? At the surface of the protein 
> may be a missing water molecule in between them?
> >
> > -Justin
> >
> >> Abdullah
> >>  


> >> From: x.peri...@rug.nl
> >> To: gmx-users@gromacs.org
> >> Subject: Re: [gmx-users] Unneccessary bonding
> >> Date: Mon, 3 May 2010 18:00:43 +0200
> >> On May 3, 2010, at 5:52 PM, abdullah ahmed wrote:
> >> Thank you very much for your reply, I agree it is probably a
> >> visualization of the effect, and that there
> >> is no bond. However, the distance between the two atoms
> >> participating in this "phantom bond" is 1.4 A°. Isn't that too
> >> close? Shouldn't it be considered a clash? 1.4 is short for
> >> sure! an H-bond goes down to 1.0 ... and charged ions make
> >> (depending on their size) bonds with water oxygen around  
2.0 ... If

> >> you have two opposite charges in front of each other that might
> >> well be happening! What kind of atoms are the ones getting
> >> close? Abdullah
> >>  


> >> From: x.peri...@rug.nl 
> >> To: gmx-users@gromacs.org 
> >> Subject: Re: [gmx-users] Unneccessary bonding
> >> Date: Mon, 3 May 2010 17:36:29 +0200
> >> On May 3, 2010, at 5:16 PM, abdullah ahmed wrote:
> >> Hello, I am a new user to GROMACS and so this
> >> question maybe somewhat
> >> naive. My objective is to run a few steps of
> >> minimization on a PDB
> >> structure and then obtain the energy value. To do so I ran the
> >> procedure suggested in the tutorial called "speptide" using
> >> the
> >> .mdp file provided in this procedure. The
> >> structure I am using has two oppositely charged residues
> >> facing each other. The initial distance(3.2 A°) is such that
> >> ionic interactions should occur between them, thereby
> >> creating a
> >> low coloumb energy score after minimization/molecular dynamics
> >> (check by looking at the log-file). However, a covalent bond
> >> is
> >> being created between them instead. This should not be
> >> happening. What do you mean a covalent bond is being created!
> >> This is basically
> >> not possible! Would that just be a visualization effect?
> >> This could result from
> >> the fact that the two atoms
> >> get really close to each other and thereby your visualization
> >> program thinks it is a covalent
> >> bond.
> >> Does anyone have any ideas on what may be happening and how I
> >> can fix it? If this information is not sufficient,
> >> please let me know, and
> >> thank you in advance.
> >> Abdullah Ahmed
> >>  


> >> Hotmail: Free, trusted and rich email service. Get it now.
> >>  --
> >> gmx-users mailing list gmx-users@gromacs.org
> >> 
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive
> >> at http://www.gromacs.org/search before posting!
> >> Please don't post (un)subscribe requests to the list. Use
> >> the www interface or send it to gmx-users-requ...@gromacs.org
> >> .

RE: [gmx-users] electrostatic interactions

[abdullah ahmed]

Actually I'd just like to know why both structures have such similar coloumb 
energy values. 
If an electro-static interaction is being made in one structure and not in the 
other then their coloumb energy values should be different too, no? Wouldn't 
this be visible with simple energy minimisation?  
I would prefer to not do molecular dynamics, because the structure is 
biologically optimal in this conformation and molecular dynamics may move it 
too much.  
  
_
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Re: [gmx-users] electrostatic interactions

[XAvier Periole]

On May 3, 2010, at 6:40 PM, abdullah ahmed wrote:

Actually I'd just like to know why both structures have such similar  
coloumb energy values.
If an electro-static interaction is being made in one structure and  
not in the other then their coloumb energy values should be  
different too, no? Wouldn't this be visible with simple energy  
minimisation?

How different are they?

You mention you use encad with "full solvent". Does that mean you ahve  
the protein

solvated in a box of water?

If your point is only to show that in one case you have an  
electrostatic interaction and not
in the other you might just need to show that with an image! The  
energies after minimization

are not necessarily more meaningful ...

I would prefer to not do molecular dynamics, because the structure  
is biologically optimal in this conformation and molecular dynamics  
may move it too much.


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[gmx-users] POPC 53a6 topology (dihedral multiplicity)

[Alex Smolyanitsky]

Hello everyone,

I am trying to include a POPC 53a6 topology from LipidsForGro96_53a6.zip (
http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies)
for a simple lipid in water sim (gromacs version 4.0.5).

I am using the lipid coordinates from the same archive and here's my
topology:
***
#include "ffG53a6.itp"
#include "popc_53a6.itp"
#include "spc.itp"

[ system ]
;Name
test

[ molecules ]
POPC  128
SOL   3585
***

grompp throws a fatal error: " Value of 'multiplicity' in Proper Dih. is 0,
which is smaller than the minimum of 1" without any prior warnings.
The error has to do with two dihedral angles with zero multiplicity:

...
22   23   24   25   1   90   -5.685   0
...
24   25   26   27   1   90   -5.685   0
...

So I looked at an ancient POPC topology for GROMOS87 and these dihedrals
have zero equilibrium angle and a multiplicity of 3:

 ...
22   23   24   25   1   0.0   5.858   3
...
24   25   26   27   1   0.0   5.858   3
...

Did the author of the 53a6 topology want to simply remove these dihedrals by
setting a multiplicity of zero? Or, should these two be set according to the
older topology? I know similar questions have been asked here in the past,
but I really want to make sure my topology is sane. Thanks a lot.

Alex
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Re: [gmx-users] POPC 53a6 topology (dihedral multiplicity)

[XAvier Periole]

HAve look at the paper describing the topology ...


On May 3, 2010, at 6:52 PM, Alex Smolyanitsky wrote:


Hello everyone,

I am trying to include a POPC 53a6 topology from  
LipidsForGro96_53a6.zip ( http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies 
 ) for a simple lipid in water sim (gromacs version 4.0.5).


I am using the lipid coordinates from the same archive and here's my  
topology:

***
#include "ffG53a6.itp"
#include "popc_53a6.itp"
#include "spc.itp"

[ system ]
;Name
test

[ molecules ]
POPC  128
SOL   3585
***

grompp throws a fatal error: " Value of 'multiplicity' in Proper  
Dih. is 0, which is smaller than the minimum of 1" without any prior  
warnings.

The error has to do with two dihedral angles with zero multiplicity:

...
22   23   24   25   1   90   -5.685   0
...
24   25   26   27   1   90   -5.685   0
...

So I looked at an ancient POPC topology for GROMOS87 and these  
dihedrals have zero equilibrium angle and a multiplicity of 3:


...
22   23   24   25   1   0.0   5.858   3
...
24   25   26   27   1   0.0   5.858   3
...

Did the author of the 53a6 topology want to simply remove these  
dihedrals by setting a multiplicity of zero? Or, should these two be  
set according to the older topology? I know similar questions have  
been asked here in the past, but I really want to make sure my  
topology is sane. Thanks a lot.


Alex
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RE: [gmx-users] electrostatic interactions

[abdullah ahmed]

I wish I could use a picture :)
Unfortunately, this is not possible since I need the energy value to be able to 
compare this to other mutations of the same structure and to provide a 
"measure" of how energetically favourable one is in comparison to the other.

And I am using a box of water because I feel that provides a better estimation 
of natural conditions than a vaccum :)
  
  
_
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Re: [gmx-users] electrostatic interactions

[XAvier Periole]

On May 3, 2010, at 7:01 PM, abdullah ahmed wrote:


I wish I could use a picture :)
Unfortunately, this is not possible since I need the energy value to  
be able to compare this to other mutations of the same structure and  
to provide a "measure" of how energetically favourable one is in  
comparison to the other.
Ok, that is what I was suspecting ... then you should be really  
careful in using the minimized
energy as a "measure" of the different effect of the mutations in  
protein. This has probably

not much value!
You'd need to go to the free energy and not the enthalpy (potential  
energy) of one minimized frame


And I am using a box of water because I feel that provides a better  
estimation of natural conditions than a vaccum :)
In that case I am afraid the water should be relaxed ... equilibrated  
if you prefer.
Its interaction with the protein is probably no-sense. A minimization  
is not

sufficient to fix it.





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Re: [gmx-users] POPC 53a6 topology (dihedral multiplicity)

[Alex Smolyanitsky]

Yup, those are indeed constants associated with phi2 (Fig. 1(B)), thanks.

Just in case anyone else is faced with the same issue, as far as forces are
concerned, these dihedrals can be commented out. When considering the energy
associated with dihedrals, just shift it appropriately.
On Mon, May 3, 2010 at 10:57 AM, XAvier Periole  wrote:

>
> HAve look at the paper describing the topology ...
>
>
>   On May 3, 2010, at 6:52 PM, Alex Smolyanitsky wrote:
>
>   Hello everyone,
>
> I am trying to include a POPC 53a6 topology from LipidsForGro96_53a6.zip (
> http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies)
>  for a simple lipid in water sim (gromacs version 4.0.5).
>
> I am using the lipid coordinates from the same archive and here's my
> topology:
> ***
> #include "ffG53a6.itp"
> #include "popc_53a6.itp"
> #include "spc.itp"
>
> [ system ]
> ;Name
> test
>
> [ molecules ]
> POPC  128
> SOL   3585
> ***
>
> grompp throws a fatal error: " Value of 'multiplicity' in Proper Dih. is 0,
> which is smaller than the minimum of 1" without any prior warnings.
> The error has to do with two dihedral angles with zero multiplicity:
>
> ...
> 22   23   24   25   1   90   -5.685   0
> ...
> 24   25   26   27   1   90   -5.685   0
> ...
>
> So I looked at an ancient POPC topology for GROMOS87 and these dihedrals
> have zero equilibrium angle and a multiplicity of 3:
>
>  ...
> 22   23   24   25   1   0.0   5.858   3
> ...
> 24   25   26   27   1   0.0   5.858   3
> ...
>
> Did the author of the 53a6 topology want to simply remove these dihedrals
> by setting a multiplicity of zero? Or, should these two be set according to
> the older topology? I know similar questions have been asked here in the
> past, but I really want to make sure my topology is sane. Thanks a lot.
>
> Alex
> --
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[gmx-users] trjconv => -[no]vel => print out the velocity ?

[Chih-Ying Lin]

Hi
Trjconv => with option   "- [no] vel "

what does the bracket "no" mean ?


with the following command,
trjconv -f MD.trr -s MD.tpr  -vel   -o MD-test.gro


the velocity is not print out on MD-test.gro.

How to print out both the velocity and trajectory at the same time from .trr
file?


THank you
Lin
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Re: [gmx-users] trjconv => -[no]vel => print out the velocity ?

[Justin A. Lemkul]

Chih-Ying Lin wrote:




Hi
Trjconv => with option   "- [no] vel "

what does the bracket "no" mean ?



It indicates a boolean: -novel means do not write velocities, -vel means write 
velocities.  Therefore, the presence or absence of a prefixed "no" determines 
the value.




with the following command,
trjconv -f MD.trr -s MD.tpr  -vel   -o MD-test.gro


the velocity is not print out on MD-test.gro.

How to print out both the velocity and trajectory at the same time from 
.trr file?




Did you actually save velocities in the .trr file (using nstvout > 0 in the .mdp 
file)?  Does gmxcheck indicate that there are velocities in the .trr file?


-Justin



THank you
Lin






--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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RE: [gmx-users] POPC 53a6 topology (dihedral multiplicity)

[Kukol, Andreas]

Hi,

The POPC_53a6 topology works only with Gromacs versions lower than 4. Please 
find attached the topology compatible with Gromacs4.

I shall update files on the Gromacs website. Sorry for causing confusion.

Best wishes
Andreas


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Alex Smolyanitsky [asmol...@asu.edu]
Sent: 03 May 2010 18:22
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] POPC 53a6 topology (dihedral multiplicity)

Yup, those are indeed constants associated with phi2 (Fig. 1(B)), thanks.

Just in case anyone else is faced with the same issue, as far as forces are 
concerned, these dihedrals can be commented out. When considering the energy 
associated with dihedrals, just shift it appropriately.
On Mon, May 3, 2010 at 10:57 AM, XAvier Periole 
mailto:x.peri...@rug.nl>> wrote:

HAve look at the paper describing the topology ...


On May 3, 2010, at 6:52 PM, Alex Smolyanitsky wrote:

Hello everyone,

I am trying to include a POPC 53a6 topology from LipidsForGro96_53a6.zip ( 
http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies
 ) for a simple lipid in water sim (gromacs version 4.0.5).

I am using the lipid coordinates from the same archive and here's my topology:
***
#include "ffG53a6.itp"
#include "popc_53a6.itp"
#include "spc.itp"

[ system ]
;Name
test

[ molecules ]
POPC  128
SOL   3585
***

grompp throws a fatal error: " Value of 'multiplicity' in Proper Dih. is 0, 
which is smaller than the minimum of 1" without any prior warnings.
The error has to do with two dihedral angles with zero multiplicity:

...
22   23   24   25   1   90   -5.685   0
...
24   25   26   27   1   90   -5.685   0
...

So I looked at an ancient POPC topology for GROMOS87 and these dihedrals have 
zero equilibrium angle and a multiplicity of 3:

...
22   23   24   25   1   0.0   5.858   3
...
24   25   26   27   1   0.0   5.858   3
...

Did the author of the 53a6 topology want to simply remove these dihedrals by 
setting a multiplicity of zero? Or, should these two be set according to the 
older topology? I know similar questions have been asked here in the past, but 
I really want to make sure my topology is sane. Thanks a lot.

Alex
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popcGromacs4_53a6.itp
Description: popcGromacs4_53a6.itp
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Re: [gmx-users] POPC 53a6 topology (dihedral multiplicity)

[Alex Smolyanitsky]

Thanks Andreas.

Is there any difference force-wise between this and our little workaround?

Alex


On Mon, May 3, 2010 at 2:17 PM, Kukol, Andreas  wrote:

> Hi,
>
> The POPC_53a6 topology works only with Gromacs versions lower than 4.
> Please find attached the topology compatible with Gromacs4.
>
> I shall update files on the Gromacs website. Sorry for causing confusion.
>
> Best wishes
> Andreas
>
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On
> Behalf Of Alex Smolyanitsky [asmol...@asu.edu]
> Sent: 03 May 2010 18:22
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] POPC 53a6 topology (dihedral multiplicity)
>
> Yup, those are indeed constants associated with phi2 (Fig. 1(B)), thanks.
>
> Just in case anyone else is faced with the same issue, as far as forces are
> concerned, these dihedrals can be commented out. When considering the energy
> associated with dihedrals, just shift it appropriately.
> On Mon, May 3, 2010 at 10:57 AM, XAvier Periole  x.peri...@rug.nl>> wrote:
>
> HAve look at the paper describing the topology ...
>
>
> On May 3, 2010, at 6:52 PM, Alex Smolyanitsky wrote:
>
> Hello everyone,
>
> I am trying to include a POPC 53a6 topology from LipidsForGro96_53a6.zip (
> http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies)
>  for a simple lipid in water sim (gromacs version 4.0.5).
>
> I am using the lipid coordinates from the same archive and here's my
> topology:
> ***
> #include "ffG53a6.itp"
> #include "popc_53a6.itp"
> #include "spc.itp"
>
> [ system ]
> ;Name
> test
>
> [ molecules ]
> POPC  128
> SOL   3585
> ***
>
> grompp throws a fatal error: " Value of 'multiplicity' in Proper Dih. is 0,
> which is smaller than the minimum of 1" without any prior warnings.
> The error has to do with two dihedral angles with zero multiplicity:
>
> ...
> 22   23   24   25   1   90   -5.685   0
> ...
> 24   25   26   27   1   90   -5.685   0
> ...
>
> So I looked at an ancient POPC topology for GROMOS87 and these dihedrals
> have zero equilibrium angle and a multiplicity of 3:
>
> ...
> 22   23   24   25   1   0.0   5.858   3
> ...
> 24   25   26   27   1   0.0   5.858   3
> ...
>
> Did the author of the 53a6 topology want to simply remove these dihedrals
> by setting a multiplicity of zero? Or, should these two be set according to
> the older topology? I know similar questions have been asked here in the
> past, but I really want to make sure my topology is sane. Thanks a lot.
>
> Alex
> --
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[gmx-users] the problem of the periodic boundary

[kecy_wu]

Hello, I use the 2D periodic boundary along the x and y axises, it 
has a strange thing. my solvent is dodecane,  I view the 
output  trajectory in the VMD, for one molecule, it has some part in 
the left(top), and some in the right(bottom), it still connections to each 
other, how to solve this problem?
 
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Re: [gmx-users] the problem of the periodic boundary

[Justin A. Lemkul]

kecy...@sina.com wrote:
Hello, I use the 2D periodic boundary along the x and y axises, it has a 
strange thing. my solvent is dodecane,  I view the output  trajectory in 
the VMD, for one molecule, it has some part in


the left(top), and some in the right(bottom), it still connections to 
each other, how to solve this problem?




Sounds to me like the normal outcome of PBC:

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

-Justin

 


Thank you !



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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