subject:"\[gmx\-users\] Re\: Alternative TRP residue"

Re: [gmx-users] Re: Alternative TRP residue

2009-06-13 Thread Justin A. Lemkul




abelius wrote:
Since the charges / bond lengths and angles were obtained for QM 
calculations for the excited state of TRP I'm wondering if it would make 
sense to apply the alternative bond lengths and keep the force constants 
of TRP in the ground state?


I guess it's really going to depend on whether or not any of the bonded 
interactions are altered by this excited state.  If, for example, your excited 
state changes the bond order of a particular bond (i.e., promotion of an 
electron in a bonded orbital to one in an antibonding orbital), then I would 
argue that the force constants in the force field are incorrect, since that bond 
would thus be weakened.


-Justin


Cheers,
Abel

Justin A. Lemkul wrote:



abelius wrote:


But How can I determine this constant? (I guess using the one of 
normal TRP would make no sense)


I would suggest reading the primary literature for your force field of 
interest.  How did the original authors assign these parameters?  
Usually bonded information comes from experimental data (spectroscopy, 
etc.)


-Justin


Thanks,
Abel



Justin A. Lemkul wrote:



abelius wrote:

Thank you for your reply,

I was just struggling to get the ffxxxbon.rtp syntax right since I 
only have atom distances to create the bonds.
So can anyone tell me what the correct syntax is for these defines 
in the ffxxxbon.rtp file?


#define   



? = force constant


Furthermore where and how can I add the angle information?



Angles are defined similarly

#define   

-Justin


Thanks,
Abel


Gerrit Groenhof wrote:

You can use #define's

Like
[ bonds ]
C1 C2 e_c1c2

Then in the ffxxxbon.rtp
 you define these things explicitly

#define e_c1c2 0.15 123445

Gerrit










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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] Re: Alternative TRP residue

2009-06-13 Thread Omer Markovitch

How many letters for residue name are allowed in the PDB format? Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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Re: [gmx-users] Re: Alternative TRP residue

2009-06-12 Thread abelius

Since the charges / bond lengths and angles were obtained for QM 
calculations for the excited state of TRP I'm wondering if it would make 
sense to apply the alternative bond lengths and keep the force constants 
of TRP in the ground state?

Cheers,
Abel

Justin A. Lemkul wrote:



abelius wrote:


But How can I determine this constant? (I guess using the one of 
normal TRP would make no sense)


I would suggest reading the primary literature for your force field of 
interest.  How did the original authors assign these parameters?  
Usually bonded information comes from experimental data (spectroscopy, 
etc.)


-Justin


Thanks,
Abel



Justin A. Lemkul wrote:



abelius wrote:

Thank you for your reply,

I was just struggling to get the ffxxxbon.rtp syntax right since I 
only have atom distances to create the bonds.
So can anyone tell me what the correct syntax is for these defines 
in the ffxxxbon.rtp file?


#define   



? = force constant


Furthermore where and how can I add the angle information?



Angles are defined similarly

#define   

-Justin


Thanks,
Abel


Gerrit Groenhof wrote:

You can use #define's

Like
[ bonds ]
C1 C2 e_c1c2

Then in the ffxxxbon.rtp
 you define these things explicitly

#define e_c1c2 0.15 123445

Gerrit










___
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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www interface or send it to gmx-users-requ...@gromacs.org.

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Re: [gmx-users] Re: Alternative TRP residue

2009-06-12 Thread Justin A. Lemkul




abelius wrote:


But How can I determine this constant? (I guess using the one of normal 
TRP would make no sense)


I would suggest reading the primary literature for your force field of interest. 
 How did the original authors assign these parameters?  Usually bonded 
information comes from experimental data (spectroscopy, etc.)


-Justin


Thanks,
Abel



Justin A. Lemkul wrote:



abelius wrote:

Thank you for your reply,

I was just struggling to get the ffxxxbon.rtp syntax right since I 
only have atom distances to create the bonds.
So can anyone tell me what the correct syntax is for these defines in 
the ffxxxbon.rtp file?


#define   



? = force constant


Furthermore where and how can I add the angle information?



Angles are defined similarly

#define   

-Justin


Thanks,
Abel


Gerrit Groenhof wrote:

You can use #define's

Like
[ bonds ]
C1 C2 e_c1c2

Then in the ffxxxbon.rtp
 you define these things explicitly

#define e_c1c2 0.15 123445

Gerrit








--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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 search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] Re: Alternative TRP residue

2009-06-12 Thread abelius



But How can I determine this constant? (I guess using the one of normal 
TRP would make no sense)

Thanks,
Abel



Justin A. Lemkul wrote:



abelius wrote:

Thank you for your reply,

I was just struggling to get the ffxxxbon.rtp syntax right since I 
only have atom distances to create the bonds.
So can anyone tell me what the correct syntax is for these defines in 
the ffxxxbon.rtp file?


#define   



? = force constant


Furthermore where and how can I add the angle information?



Angles are defined similarly

#define   

-Justin


Thanks,
Abel


Gerrit Groenhof wrote:

You can use #define's

Like
[ bonds ]
C1 C2 e_c1c2

Then in the ffxxxbon.rtp
 you define these things explicitly

#define e_c1c2 0.15 123445

Gerrit





___
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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Re: [gmx-users] Re: Alternative TRP residue

2009-06-12 Thread Justin A. Lemkul




abelius wrote:

Thank you for your reply,

I was just struggling to get the ffxxxbon.rtp syntax right since I only 
have atom distances to create the bonds.
So can anyone tell me what the correct syntax is for these defines in 
the ffxxxbon.rtp file?


#define   



? = force constant


Furthermore where and how can I add the angle information?



Angles are defined similarly

#define   

-Justin


Thanks,
Abel


Gerrit Groenhof wrote:

You can use #define's

Like
[ bonds ]
C1 C2 e_c1c2

Then in the ffxxxbon.rtp
 you define these things explicitly

#define e_c1c2 0.15 123445

Gerrit



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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 
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Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] Re: Alternative TRP residue

2009-06-12 Thread abelius


Thank you for your reply,

I was just struggling to get the ffxxxbon.rtp syntax right since I only 
have atom distances to create the bonds.
So can anyone tell me what the correct syntax is for these defines in 
the ffxxxbon.rtp file?


#define   

Furthermore where and how can I add the angle information?

Thanks,
Abel


Gerrit Groenhof wrote:

You can use #define's

Like
[ bonds ]
C1 C2 e_c1c2

Then in the ffxxxbon.rtp
 you define these things explicitly

#define e_c1c2 0.15 123445

Gerrit


On 11 Jun 2009, at 17:31, gmx-users-requ...@gromacs.org wrote:


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Today's Topics:

  1. Re: Re: gmx-users Digest, Vol 62, Issue 57 (Justin A. Lemkul)
  2. Re: gromacs-4.0.5 parallel run in 8 cpu: slow speed (Thamu)
  3. Alternative TRP residue (abelius)
  4. Re: Issues regarding exclusions and Charge groupdistribution
 (Manik Mayur)


--

Message: 1
Date: Thu, 11 Jun 2009 10:50:29 -0400
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 62, Issue 57
To: Discussion list for GROMACS users 
Message-ID: <4a3119b5.30...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



Thamu wrote:

Hi Mark,

Yes I have compared the runtime for single as well as 8 processor .
Could you please tell me the right steps to configure GROMACS-MPI 
version?.




The full installation procedure is here:

http://oldwww.gromacs.org/content/view/23/33/

...as well as Appendix A of the manual.

-Justin


Thanks.

thamu

2009/6/11 mailto:gmx-users-requ...@gromacs.org>>

   Send gmx-users mailing list submissions to
  gmx-users@gromacs.org 

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   You can reach the person managing the list at
  gmx-users-ow...@gromacs.org 



   When replying, please edit your Subject line so it is more specific
   than "Re: Contents of gmx-users digest..."


   Today's Topics:

 1. Re: gromacs-4.0.5 parallel run in 8 cpu: slow speed (Mark 
Abraham)



   
--


   Message: 1
   Date: Thu, 11 Jun 2009 13:56:15 + (GMT)
   From: Mark Abraham mailto:mark.abra...@anu.edu.au>>
   Subject: Re: [gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow
  speed
   To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
   Message-ID: mailto:fbe6b07c8ea.4a310...@anu.edu.au>>
   Content-Type: text/plain; charset="iso-8859-1"

   On 06/11/09, Thamu  mailto:asth...@gmail.com>>
   wrote:


Hi Mark,

The top md.log is below. The mdrun command was "mpirun -np 8

   ~/software/bin/mdrun_mpi -deffnm md"
   In my experience, correctly-configured MPI gromacs running in
   parallel reports information about the number of nodes and the
   identity of the node writing the .log file. This is missing, so
   something is wrong with your setup.

   I've assumed that you've compared this "8-processor" runtime with a
   single-processor runtime and found them comparable...

   Mark





 :-)   G  R  O  M  A  C  S  (-:

 GROup of MAchos and Cynical Suckers

:-)   VERSION 4.0.5  (-:


 Written by David van der Spoel, Erik Lindahl, Berk Hess,

   and others.

  Copyright (c) 1991-2000, University of Groningen, The

   Netherlands.

Copyright (c) 2001-2008, The GROMACS development team,
   check out http://www.gromacs.org

   (http://www.gromacs.org) for more information.


This program is free software; you can redistribute it

   and/or

 modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either

   version 2

of the License, or (at your option) any later version.

  :-)   /home/thamu/software/bin/mdrun_mpi  (-:


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and

   scalable

molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
D. va

[gmx-users] Re: Alternative TRP residue

2009-06-11 Thread Gerrit Groenhof


You can use #define's

Like
[ bonds ]
C1 C2 e_c1c2

Then in the ffxxxbon.rtp
 you define these things explicitly

#define e_c1c2 0.15 123445

Gerrit


On 11 Jun 2009, at 17:31, gmx-users-requ...@gromacs.org wrote:


Send gmx-users mailing list submissions to
gmx-users@gromacs.org

To subscribe or unsubscribe via the World Wide Web, visit
http://lists.gromacs.org/mailman/listinfo/gmx-users
or, via email, send a message with subject or body 'help' to
gmx-users-requ...@gromacs.org

You can reach the person managing the list at
gmx-users-ow...@gromacs.org

When replying, please edit your Subject line so it is more specific
than "Re: Contents of gmx-users digest..."


Today's Topics:

  1. Re: Re: gmx-users Digest, Vol 62, Issue 57 (Justin A. Lemkul)
  2. Re: gromacs-4.0.5 parallel run in 8 cpu: slow speed (Thamu)
  3. Alternative TRP residue (abelius)
  4. Re: Issues regarding exclusions and Charge group   distribution
 (Manik Mayur)


--

Message: 1
Date: Thu, 11 Jun 2009 10:50:29 -0400
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 62, Issue 57
To: Discussion list for GROMACS users 
Message-ID: <4a3119b5.30...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



Thamu wrote:

Hi Mark,

Yes I have compared the runtime for single as well as 8 processor .
Could you please tell me the right steps to configure GROMACS-MPI  
version?.




The full installation procedure is here:

http://oldwww.gromacs.org/content/view/23/33/

...as well as Appendix A of the manual.

-Justin


Thanks.

thamu

2009/6/11 mailto:gmx-users-requ...@gromacs.org>>

   Send gmx-users mailing list submissions to
  gmx-users@gromacs.org 

   To subscribe or unsubscribe via the World Wide Web, visit
  http://lists.gromacs.org/mailman/listinfo/gmx-users
   or, via email, send a message with subject or body 'help' to
  gmx-users-requ...@gromacs.org
   

   You can reach the person managing the list at
  gmx-users-ow...@gromacs.org 


   When replying, please edit your Subject line so it is more  
specific

   than "Re: Contents of gmx-users digest..."


   Today's Topics:

 1. Re: gromacs-4.0.5 parallel run in 8 cpu: slow speed (Mark  
Abraham)




--


   Message: 1
   Date: Thu, 11 Jun 2009 13:56:15 + (GMT)
   From: Mark Abraham mailto:mark.abra...@anu.edu.au>>
   Subject: Re: [gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow
  speed
   To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
   Message-ID: mailto:fbe6b07c8ea.4a310...@anu.edu.au>>
   Content-Type: text/plain; charset="iso-8859-1"

   On 06/11/09, Thamu  mailto:asth...@gmail.com>>
   wrote:


Hi Mark,

The top md.log is below. The mdrun command was "mpirun -np 8

   ~/software/bin/mdrun_mpi -deffnm md"
   In my experience, correctly-configured MPI gromacs running in
   parallel reports information about the number of nodes and the
   identity of the node writing the .log file. This is missing, so
   something is wrong with your setup.

   I've assumed that you've compared this "8-processor" runtime  
with a

   single-processor runtime and found them comparable...

   Mark





 :-)   G  R  O  M  A  C  S  (-:

 GROup of MAchos and Cynical Suckers

:-)   VERSION 4.0.5  (-:


 Written by David van der Spoel, Erik Lindahl, Berk Hess,

   and others.

  Copyright (c) 1991-2000, University of Groningen, The

   Netherlands.

Copyright (c) 2001-2008, The GROMACS development team,
   check out http://www.gromacs.org

   (http://www.gromacs.org) for more information.


This program is free software; you can redistribute it

   and/or

 modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either

   version 2

of the License, or (at your option) any later version.

  :-)   /home/thamu/software/bin/mdrun_mpi  (-:


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and

   scalable

molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark

   and H. J. C.

Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.

Re: [gmx-users] Re: Alternative TRP residue

Re: [gmx-users] Re: Alternative TRP residue

Re: [gmx-users] Re: Alternative TRP residue

Re: [gmx-users] Re: Alternative TRP residue

Re: [gmx-users] Re: Alternative TRP residue

Re: [gmx-users] Re: Alternative TRP residue

Re: [gmx-users] Re: Alternative TRP residue

[gmx-users] Re: Alternative TRP residue

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