subject:"RE\: \[gmx\-users\] Position Restraints"

Ohhh...! :-)
I could not get it on my own independently!
Thanks for all your explanation! Many many thanks.

Sincerely,
Shima

- Original Message -
From: Justin Lemkul 
To: Discussion list for GROMACS users 
Cc: 
Sent: Tuesday, March 26, 2013 12:02 AM
Subject: Re: [gmx-users] position restraints

On 3/25/13 3:25 PM, Shima Arasteh wrote:
> Dear Justin,
> 
> As I got, I need to edit the lipid_posre.itp file. To do so, I need to change 
> numbering of position restraining in lipid_posre.itp file to what they are in 
> their original itp file: In my case popc.itp file.
> Am I right?
> 

More or less, but for the sake of clarity, let me explain this fully so you can 
hopefully arrive at a resolution quickly.  Say I have a system of arbitrary 
molecules that have 4 atoms each.  Position restraints only work per 
[moleculetype], so using genrestr is somewhat dangerous unless you are working 
with a coordinate file or suitable index file that only specifies a single 
molecule.  Otherwise, the selection is rather ham-handed and actually gives you 
a nonfunctional .itp file (hence the WARNING in the help description). 
Therefore, I can only use atom numbers 1, 2, 3, and 4 in my 
[position_restraints] directive.  Anything above 4 (i.e. based on selecting 
multiple molecules in genrestr) triggers a fatal error.

What then happens is that grompp reads those atoms, and every time it 
encounters those atom numbers within the [moleculetype] (irrespective of how 
many times that molecule appears), restraints are applied as specified.

So, if you want to restrain only P atoms of every POPC molecule, you basically 
need a one-line .itp file.  If, for instance, P is atom number 8:

[ position_restraints ]
   8   1   0    0    1000

That will restrain all P atoms (every time they occur, as grompp finds them 
throughout the coordinate file) in the z-dimension only.  Hopefully that all 
makes sense and this experience has been educational as far as how these things 
work.

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
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] position restraints




On 3/25/13 3:25 PM, Shima Arasteh wrote:

Dear Justin,

As I got, I need to edit the lipid_posre.itp file. To do so, I need to change 
numbering of position restraining in lipid_posre.itp file to what they are in 
their original itp file: In my case popc.itp file.
Am I right?



More or less, but for the sake of clarity, let me explain this fully so you can 
hopefully arrive at a resolution quickly.  Say I have a system of arbitrary 
molecules that have 4 atoms each.  Position restraints only work per 
[moleculetype], so using genrestr is somewhat dangerous unless you are working 
with a coordinate file or suitable index file that only specifies a single 
molecule.  Otherwise, the selection is rather ham-handed and actually gives you 
a nonfunctional .itp file (hence the WARNING in the help description). 
Therefore, I can only use atom numbers 1, 2, 3, and 4 in my 
[position_restraints] directive.  Anything above 4 (i.e. based on selecting 
multiple molecules in genrestr) triggers a fatal error.


What then happens is that grompp reads those atoms, and every time it encounters 
those atom numbers within the [moleculetype] (irrespective of how many times 
that molecule appears), restraints are applied as specified.


So, if you want to restrain only P atoms of every POPC molecule, you basically 
need a one-line .itp file.  If, for instance, P is atom number 8:


[ position_restraints ]
   8   1   001000

That will restrain all P atoms (every time they occur, as grompp finds them 
throughout the coordinate file) in the z-dimension only.  Hopefully that all 
makes sense and this experience has been educational as far as how these things 
work.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] position restraints

Dear Justin,

As I got, I need to edit the lipid_posre.itp file. To do so, I need to change 
numbering of position restraining in lipid_posre.itp file to what they are in 
their original itp file: In my case popc.itp file.
Am I right? 

Sincerely,
Shima

- Original Message -
From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS 
users 
Cc: 
Sent: Monday, March 25, 2013 11:34 PM
Subject: Re: [gmx-users] position restraints

On 3/25/13 3:00 PM, Shima Arasteh wrote:
> Yes, you are right. Because I have read the include mechanism in website many 
> times, but I dont undrestand it in deep! :-(
> I may need to study more.

I would again suggest focusing more on the position restraints contents 
themselves.  Your formulation for #including them is correct.  The contents of 
lipid_posre.itp are not.  There is substantial discussion on the topic of 
position restraints in the manual, as well as the help description of genrestr 
(especially the part that starts with "WARNING"), which I am willing to bet 
will solve your issues if you read it carefully.

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
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] position restraints




On 3/25/13 3:00 PM, Shima Arasteh wrote:

Yes, you are right. Because I have read the include mechanism in website many 
times, but I dont undrestand it in deep! :-(
I may need to study more.


I would again suggest focusing more on the position restraints contents 
themselves.  Your formulation for #including them is correct.  The contents of 
lipid_posre.itp are not.  There is substantial discussion on the topic of 
position restraints in the manual, as well as the help description of genrestr 
(especially the part that starts with "WARNING"), which I am willing to bet will 
solve your issues if you read it carefully.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] position restraints

Yes, you are right. Because I have read the include mechanism in website many 
times, but I dont undrestand it in deep! :-( 
I may need to study more.
Thanks

Sincerely,
Shima

- Original Message -
From: Justin Lemkul 
To: Discussion list for GROMACS users 
Cc: 
Sent: Monday, March 25, 2013 11:20 PM
Subject: Re: [gmx-users] position restraints

On 3/25/13 2:47 PM, Shima Arasteh wrote:
> Would you please let me know that what subject I need to look for through 
> manual or threads? Making index groups of multiple atoms?
> 

What you need to understand is how the position restraint mechanism works.  If 
you know that, you can make .itp files by hand using a text editor if you like 
(which is actually what I do in the case of one-liners like lipid_posre.itp for 
what you're doing).

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
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] position restraints




On 3/25/13 2:47 PM, Shima Arasteh wrote:

Would you please let me know that what subject I need to look for through 
manual or threads? Making index groups of multiple atoms?



What you need to understand is how the position restraint mechanism works.  If 
you know that, you can make .itp files by hand using a text editor if you like 
(which is actually what I do in the case of one-liners like lipid_posre.itp for 
what you're doing).


-Justin


--


Justin A. Lemkul, Ph.D.
Research Scientist
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] position restraints

Would you please let me know that what subject I need to look for through 
manual or threads? Making index groups of multiple atoms?


Thanks for your suggestions.

 
Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS 
users 
Cc: 
Sent: Monday, March 25, 2013 10:22 PM
Subject: Re: [gmx-users] position restraints



On 3/25/13 1:50 PM, Shima Arasteh wrote:
> Yes sir!
>
> What I have in my top file is :
> ; Include forcefield parameters
> #include "./charmm36-modified.ff/forcefield.itp"
>
>
> ; Include chain topologies
> #include "topol_Protein_chain_A.itp"
> #ifdef POSRES
> #include "protein_chain_A_posre.itp"
> #endif
> #include "topol_Protein_chain_B.itp"
> #ifdef POSRES
> #include "protein_chain_B_posre.itp"
> #endif
>
> ; Include POPC chain topology
> #include "popc.itp"
> #ifdef POSRES_LIPID
> #include "lipid_posre.itp"
> #endif
>
> ; Include water topology
> #include "./charmm36-modified.ff/tip3p.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>     1    1       1000       1000       1000
> #endif
>
> ; Include topology for ions
> #include "./charmm36-modified.ff/ions.itp"
>
> [ system ]
> ; Name
> Protein
>
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> Protein_chain_B     1
> POPC        238
> SOL         18706
> NA               615
> CL               617
>
>
> I used genrestr to create the itp file of P atom types.The generated itp file 
> is lipid_posre.itp. If I need to send any other information please let me 
> know.
>

In that case, lipid_posre.itp should have only one line.  If you've made an 
index group of multiple P atoms across multiple molecules, that is the 
incorrect 
approach.  Consult the manual, website, and numerous threads in the archive.

-Justin

-- 


Justin A. Lemkul, Ph.D.
Research Scientist
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] position restraints




On 3/25/13 1:50 PM, Shima Arasteh wrote:

Yes sir!

What I have in my top file is :
; Include forcefield parameters
#include "./charmm36-modified.ff/forcefield.itp"


; Include chain topologies
#include "topol_Protein_chain_A.itp"
#ifdef POSRES
#include "protein_chain_A_posre.itp"
#endif
#include "topol_Protein_chain_B.itp"
#ifdef POSRES
#include "protein_chain_B_posre.itp"
#endif

; Include POPC chain topology
#include "popc.itp"
#ifdef POSRES_LIPID
#include "lipid_posre.itp"
#endif

; Include water topology
#include "./charmm36-modified.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
11   1000   1000   1000
#endif

; Include topology for ions
#include "./charmm36-modified.ff/ions.itp"

[ system ]
; Name
Protein

[ molecules ]
; Compound#mols
Protein_chain_A 1
Protein_chain_B 1
POPC238
SOL 18706
NA   615
CL   617


I used genrestr to create the itp file of P atom types.The generated itp file 
is lipid_posre.itp. If I need to send any other information please let me know.



In that case, lipid_posre.itp should have only one line.  If you've made an 
index group of multiple P atoms across multiple molecules, that is the incorrect 
approach.  Consult the manual, website, and numerous threads in the archive.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] position restraints

Yes sir!

What I have in my top file is :
; Include forcefield parameters
#include "./charmm36-modified.ff/forcefield.itp"


; Include chain topologies
#include "topol_Protein_chain_A.itp"
#ifdef POSRES
#include "protein_chain_A_posre.itp"
#endif
#include "topol_Protein_chain_B.itp"
#ifdef POSRES
#include "protein_chain_B_posre.itp"
#endif

; Include POPC chain topology
#include "popc.itp"
#ifdef POSRES_LIPID
#include "lipid_posre.itp"
#endif

; Include water topology
#include "./charmm36-modified.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcx    fcy    fcz
   1    1   1000   1000   1000
#endif

; Include topology for ions
#include "./charmm36-modified.ff/ions.itp"

[ system ]
; Name
Protein

[ molecules ]
; Compound    #mols
Protein_chain_A 1
Protein_chain_B 1
POPC        238
SOL 18706
NA   615
CL   617


I used genrestr to create the itp file of P atom types.The generated itp file 
is lipid_posre.itp. If I need to send any other information please let me know.

 
Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Discussion list for GROMACS users 
Cc: 
Sent: Monday, March 25, 2013 10:13 PM
Subject: Re: [gmx-users] position restraints



On 3/25/13 1:40 PM, Shima Arasteh wrote:
> Believe me I add this line to mdp file as you wrote in KALP-15-DPPC.
> 

I believe what I see.  If you're trying to re-type from memory what's in your 
topology and/or .mdp file, that's not productive.  Please copy and paste to 
make efficient use of everyone's time.

> "define        = -DPOSRES_LIPID"
> 
> Also added these to top file.
> #ifdef POSRES_LIPID
> #include "lipid_posre.itp"
> #endif
>   But I get again this error that the "This probably means that you have 
>inserted topology section "position_restraints"
> in a part belonging to a different molecule than you intended to."
> 
> Why this doesn't match?? I think POSITION RESTRAINING is making me crazy! :((
> Would you please help me?
> 

I've been trying, and it appears you're either giving inconsistent or incorrect 
information.  Copy and paste directly from your .top file whatever sections are 
relevant.  You also haven't said what is in lipid_posre.itp, which can be 
another source of problems.  You just said you've created it with genrestr, but 
you didn't say what group you included.  The numbering in the position 
restraint file is per [moleculetype], not the global atom numbering in the 
coordinate file.

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
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] position restraints




On 3/25/13 1:40 PM, Shima Arasteh wrote:

Believe me I add this line to mdp file as you wrote in KALP-15-DPPC.



I believe what I see.  If you're trying to re-type from memory what's in your 
topology and/or .mdp file, that's not productive.  Please copy and paste to make 
efficient use of everyone's time.



"define= -DPOSRES_LIPID"

Also added these to top file.
#ifdef POSRES_LIPID
#include "lipid_posre.itp"
#endif
  But I get again this error that the "This probably means that you have inserted 
topology section "position_restraints"
in a part belonging to a different molecule than you intended to."

Why this doesn't match?? I think POSITION RESTRAINING is making me crazy! :((
Would you please help me?



I've been trying, and it appears you're either giving inconsistent or incorrect 
information.  Copy and paste directly from your .top file whatever sections are 
relevant.  You also haven't said what is in lipid_posre.itp, which can be 
another source of problems.  You just said you've created it with genrestr, but 
you didn't say what group you included.  The numbering in the position restraint 
file is per [moleculetype], not the global atom numbering in the coordinate file.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] position restraints

Believe me I add this line to mdp file as you wrote in KALP-15-DPPC.

"define        = -DPOSRES_LIPID "

Also added these to top file.
#ifdef POSRES_LIPID
#include "lipid_posre.itp"
#endif 
 But I get again this error that the "This probably means that you have 
inserted topology section "position_restraints"
in a part belonging to a different molecule than you intended to."

Why this doesn't match?? I think POSITION RESTRAINING is making me crazy! :((
Would you please help me? 

Thanks for help.

Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS 
users 
Cc: 
Sent: Monday, March 25, 2013 8:52 PM
Subject: Re: [gmx-users] position restraints



On 3/25/13 12:06 PM, Shima Arasteh wrote:
> Hi,
>
> I want to use position restraints on P atom types of POPC, and on my protein 
> inserted in POPC.
> The inserted protein has 2 chains.
>
> 1.
>
> I made index files for each chain and then restrained them by these commands:
> #make_ndx -f minim.gro -o protein_chain_A.ndx
> #genrestr -f minim.gro -o protein_chain_A_posre.itp -fc 10 10 10 
> -n protein_chain_A.ndx
>
> #make_ndx -f minim.gro -o protein_chain_B.ndx
> #genrestr -f minim.gro -o protein_chain_B_posre.itp -fc 10 10 10 
> -n protein_chain_B.ndx
>
> #make_ndx -f minim.gro -o lipid_posre.ndx
> #genrestr -f minim.gro -o lipid_posre.itp -fc 10 10 10 -n 
> lipid_posre.ndx
>
> 2.
>
> Then these lines added to top of the itp files:
> #ifdef POSRE
> #endif
>
> 3.
> Then restrained them as follow in top file:
>
> ; Include chain topologies
> #include "topol_Protein_chain_A.itp"
> #ifdef POSRE
> #include "protein_chain_A_posre.itp"
> #endif
> #include "topol_Protein_chain_B.itp"
> #ifdef POSRE
> #include "protein_chain_B_posre.itp"
> #endif
>
> ; Include POPC chain topology
> #include "popc.itp"
> #ifdef POSRE_LIPID
> #include "lipid_posre.itp"
> #endif
>
> 4.
>
> Also added the define statement to mdp file :
>
> define        = -DPOSRES_LIPID -DPOSRES
>
> But when I run the grompp and get the per-processed top, only the chain_A is 
> included in position restraint!
>
> Would you please give me suggestions? They would be appreciated.

Again, "POSRE" and "POSRES" are different.  -DPOSRES will not trigger the 
#ifdef 
POSRE block.

-Justin

-- 


Justin A. Lemkul, Ph.D.
Research Scientist
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] position restraints




On 3/25/13 12:06 PM, Shima Arasteh wrote:

Hi,

I want to use position restraints on P atom types of POPC, and on my protein 
inserted in POPC.
The inserted protein has 2 chains.

1.

I made index files for each chain and then restrained them by these commands:
#make_ndx -f minim.gro -o protein_chain_A.ndx
#genrestr -f minim.gro -o protein_chain_A_posre.itp -fc 10 10 10 -n 
protein_chain_A.ndx

#make_ndx -f minim.gro -o protein_chain_B.ndx
#genrestr -f minim.gro -o protein_chain_B_posre.itp -fc 10 10 10 -n 
protein_chain_B.ndx

#make_ndx -f minim.gro -o lipid_posre.ndx
#genrestr -f minim.gro -o lipid_posre.itp -fc 10 10 10 -n 
lipid_posre.ndx

2.

Then these lines added to top of the itp files:
#ifdef POSRE
#endif

3.
Then restrained them as follow in top file:

; Include chain topologies
#include "topol_Protein_chain_A.itp"
#ifdef POSRE
#include "protein_chain_A_posre.itp"
#endif
#include "topol_Protein_chain_B.itp"
#ifdef POSRE
#include "protein_chain_B_posre.itp"
#endif

; Include POPC chain topology
#include "popc.itp"
#ifdef POSRE_LIPID
#include "lipid_posre.itp"
#endif

4.

Also added the define statement to mdp file :

define= -DPOSRES_LIPID -DPOSRES

But when I run the grompp and get the per-processed top, only the chain_A is 
included in position restraint!

Would you please give me suggestions? They would be appreciated.


Again, "POSRE" and "POSRES" are different.  -DPOSRES will not trigger the #ifdef 
POSRE block.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] position restraints

2013-03-14 Thread Erik Marklund


Restraints allow, by definition, for slight deviations.

Erik

On Mar 14, 2013, at 12:51 PM, Shima Arasteh wrote:


Dear gmx users,

I want to use restraints on backbone of my protein to keep its  
secondary structure during minimization and equilibration steps. To  
do so, I generated backbone-restrain.itp and then included it to top  
file. Next, added define = -DPOSRES to minim.mdp file.
After minimization, when I check the minimization output file, I saw  
that the backbone of input and output files are not exactly the same.
Is there any step which I have not done to set the restraints  
correctly?



Thanks in advance.

Sincerely,
Shima
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Re: [gmx-users] position restraints in SMD

2012-07-16 Thread Justin Lemkul




On 7/16/12 5:36 AM, Raj wrote:

Hi all,

  It may be naive but I would like to get some clear explanation in SMD ( COM
pulling) reg. The question is, Before performing the COM-pulling (incase of
protein ligand complex) do we need to position restrain the ligand using
genrestr and then add the topology to the topol.top file. If not why should
not we restrain the ligand. Thanks in advance



The initial equilibration can be approached in a number of ways that includes 
restraining both the protein and ligand or one or the other.  Restraints are 
only intended to avoid large structural changes due to reorganization of the 
solvent.  Thus you may choose to restrain the whole complex initially and then 
reduce or remove the restraints over the course of further equilibration.  There 
are no hard and fast rules.  Look into the literature and see what others 
recommend, and evaluate for yourself whether or not such a protocol is 
reasonable in your case.


-Justin

--


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Research Scientist
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] Position Restraints of one of the moleculetpye

2012-05-29 Thread Steven Neumann

On Tue, May 29, 2012 at 12:21 PM, Justin A. Lemkul  wrote:

>
>
> On 5/29/12 6:52 AM, Steven Neumann wrote:
>
>> Ok. My topology:
>>
>> ; Include forcefield parameters
>> #include "./charmm27.ff/forcefield.itp"
>>
>> ; Include ligand topology
>> #include "ligand1.itp"
>>
>> ; Include Position restraint file
>> #ifdef POSRES_1
>> #include "posre_ligand1.itp"
>> #endif
>>
>> ; Include ligand topology
>> #include "ligand2.itp"
>>
>> ; Include Position restraint file
>> #ifdef POSRES_2
>> #include "posre_ligand2.itp"
>> #endif
>>
>> ; Include ligand topology
>> #include "ligand3.itp"
>>
>> ; Include Position restraint file
>> #ifdef POSRES_3
>> #include "posre_ligand3.itp"
>> #endif
>>
>> ; Include ligand topology
>> #include "ligand4.itp"
>>
>> ; Include Position restraint file
>> #ifdef POSRES_4
>> #include "posre_ligand4.itp"
>> #endif
>>
>>
>> ; Include ligand topology
>> #include "ligand5.itp"
>>
>> ; Include Position restraint file
>> #ifdef POSRES_5
>> #include "posre_ligand5.itp"
>> #endif
>>
>> ; Include ligand topology
>> #include "ligand6.itp"
>>
>> ; Include Position restraint file
>> #ifdef POSRES_6
>> #include "posre_ligand6.itp"
>> #endif
>>
>> ; Include water topology
>> #include "./charmm27mod.ff/tip3p.itp"
>>
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ;  i funct   fcxfcyfcz
>>11   1000   1000   1000
>> #endif
>>
>> ; Include topology for ions
>> #include "./charmm27.ff/ions.itp"
>>
>> [ system ]
>> ; Name
>> Protein in water
>>
>> [ molecules ]
>> ; Compound#mols
>> ligand1   1
>> ligand2   1
>> ligand3   1
>> ligand4   1
>> ligand5   1
>> ligand6   1
>> SOL  4617
>>
>>
>> Each ligand.itp has [moleculetype ] - ligand1...ligand6, all other
>> information
>> is the same
>>
>> posre_ligand1.itp - ... - posre_ligand2.itp are all the same files.
>>
>> Then when I grompp:
>>
>> Syntax error - File ligand2.itp, line 7
>> Last line read:
>> '[ atomtypes ] '
>> Invalid order for directive atomtypes
>>
>> Any suggestions appreciated,
>>
>>
> Once you declare a [moleculetype], the other force field-level directives
> cannot be called.  If all the ligand topologies are the same, remove
> [atomtypes] from all but the first.
>
>
> -Justin
>

Thanks Justin. Removing [pairtypes] and [atomtypes] from all but not the
first helped.

Steven



> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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] Position Restraints of one of the moleculetpye

2012-05-29 Thread Justin A. Lemkul




On 5/29/12 6:52 AM, Steven Neumann wrote:

Ok. My topology:

; Include forcefield parameters
#include "./charmm27.ff/forcefield.itp"

; Include ligand topology
#include "ligand1.itp"

; Include Position restraint file
#ifdef POSRES_1
#include "posre_ligand1.itp"
#endif

; Include ligand topology
#include "ligand2.itp"

; Include Position restraint file
#ifdef POSRES_2
#include "posre_ligand2.itp"
#endif

; Include ligand topology
#include "ligand3.itp"

; Include Position restraint file
#ifdef POSRES_3
#include "posre_ligand3.itp"
#endif

; Include ligand topology
#include "ligand4.itp"

; Include Position restraint file
#ifdef POSRES_4
#include "posre_ligand4.itp"
#endif


; Include ligand topology
#include "ligand5.itp"

; Include Position restraint file
#ifdef POSRES_5
#include "posre_ligand5.itp"
#endif

; Include ligand topology
#include "ligand6.itp"

; Include Position restraint file
#ifdef POSRES_6
#include "posre_ligand6.itp"
#endif

; Include water topology
#include "./charmm27mod.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
11   1000   1000   1000
#endif

; Include topology for ions
#include "./charmm27.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
ligand1   1
ligand2   1
ligand3   1
ligand4   1
ligand5   1
ligand6   1
SOL  4617


Each ligand.itp has [moleculetype ] - ligand1...ligand6, all other information
is the same

posre_ligand1.itp - ... - posre_ligand2.itp are all the same files.

Then when I grompp:

Syntax error - File ligand2.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes

Any suggestions appreciated,



Once you declare a [moleculetype], the other force field-level directives cannot 
be called.  If all the ligand topologies are the same, remove [atomtypes] from 
all but the first.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Position Restraints of one of the moleculetpye

2012-05-29 Thread Steven Neumann

Ok. My topology:

; Include forcefield parameters
#include "./charmm27.ff/forcefield.itp"

; Include ligand topology
#include "ligand1.itp"

; Include Position restraint file
#ifdef POSRES_1
#include "posre_ligand1.itp"
#endif

; Include ligand topology
#include "ligand2.itp"

; Include Position restraint file
#ifdef POSRES_2
#include "posre_ligand2.itp"
#endif

; Include ligand topology
#include "ligand3.itp"

; Include Position restraint file
#ifdef POSRES_3
#include "posre_ligand3.itp"
#endif

; Include ligand topology
#include "ligand4.itp"

; Include Position restraint file
#ifdef POSRES_4
#include "posre_ligand4.itp"
#endif


; Include ligand topology
#include "ligand5.itp"

; Include Position restraint file
#ifdef POSRES_5
#include "posre_ligand5.itp"
#endif

; Include ligand topology
#include "ligand6.itp"

; Include Position restraint file
#ifdef POSRES_6
#include "posre_ligand6.itp"
#endif

; Include water topology
#include "./charmm27mod.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include topology for ions
#include "./charmm27.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
ligand1   1
ligand2   1
ligand3   1
ligand4   1
ligand5   1
ligand6   1
SOL  4617


Each ligand.itp has [moleculetype ] - ligand1...ligand6, all other
information is the same

posre_ligand1.itp - ... - posre_ligand2.itp are all the same files.

Then when I grompp:

Syntax error - File ligand2.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes

Any suggestions appreciated,

Steven




On Mon, May 28, 2012 at 5:25 PM, Justin A. Lemkul  wrote:

>
>
> On 5/28/12 10:48 AM, Steven Neumann wrote:
>
>> Dear Gmx Users,
>>
>> I am fighting with the position restraints. My system cosnsists of 6
>> ligands -
>> all of them have the same topology - ligand.itp. I want to:
>>
>> 1. Run NPT restraining all of ligands (easy: -DPOSRES_L, ifdef POSRE_L,
>> posre
>> ligand1.itp
>> 2. Restrain 5 of them and pull one of them away.
>>
>> Here I came across some difficulties.
>>
>> I used genrestr -f 6ligands.gro -n index.ndx -o posre1.itp
>>
>> and by index files I create an index of the ligands I wan to restrain.
>> Each my
>> ligands has 46 atoms. When I process to grompp:
>>
>> Atom index (256) in position_restraints out of bounds (1-46).
>> This probably means that you have inserted topology section
>> "position_restraints
>>
>> Shall I rename Ligands as different residue names? If my posre includes
>> 1-46
>> atom all ligands are restraints? How to restrain just 5 out of 6 of them?
>>
>>
> Position restraints are applied on a per-moleculetype basis.  If you have
> six copies of a ligand, the only way to do this is to define the sixth as a
> special [moleculetype] (even if it contains identical information) with a
> different name, such that it can be restrained in the absence of restraints
> on the others.  See the logic here:
>
> http://www.gromacs.org/**Documentation/Errors#Atom_**index_n_in_position_*
> *restraints_out_of_bounds
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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] Position Restraints of one of the moleculetpye

2012-05-28 Thread Justin A. Lemkul

On 5/28/12 10:48 AM, Steven Neumann wrote:

Dear Gmx Users,

I am fighting with the position restraints. My system cosnsists of 6 ligands -
all of them have the same topology - ligand.itp. I want to:

1. Run NPT restraining all of ligands (easy: -DPOSRES_L, ifdef POSRE_L, posre
ligand1.itp
2. Restrain 5 of them and pull one of them away.

Here I came across some difficulties.

I used genrestr -f 6ligands.gro -n index.ndx -o posre1.itp

and by index files I create an index of the ligands I wan to restrain. Each my
ligands has 46 atoms. When I process to grompp:

Atom index (256) in position_restraints out of bounds (1-46).
This probably means that you have inserted topology section "position_restraints

Shall I rename Ligands as different residue names? If my posre includes 1-46
atom all ligands are restraints? How to restrain just 5 out of 6 of them?

Position restraints are applied on a per-moleculetype basis. If you have six
copies of a ligand, the only way to do this is to define the sixth as a special
[moleculetype] (even if it contains identical information) with a different
name, such that it can be restrained in the absence of restraints on the others.
See the logic here:

http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds

-Justin

Justin A. Lemkul, Ph.D.
Research Scientist
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] Position Restraints

2012-04-26 Thread Justin A. Lemkul




On 4/26/12 1:59 PM, Dariush Mohammadyani wrote:

Thanks dear Justin.
No, the protein is moving in right direction, but I am going to restrain any
changing the position and then monitory these movements during MD run.
I could see the Pos. Res. works in md.log file.


Then I don't understand what the problem is.  You'll have to describe what 
you're doing in greater detail.


-Justin


Regards,
Dariush

On Thu, Apr 26, 2012 at 1:38 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:



On 4/26/12 1:35 PM, Dariush Mohammadyani wrote:

Dear All,
I am using CG-MD using MARTINI forcefield. The system contains Protein
and lipid
bilayer. Although I used:
define = -DPOSRES
components in system were moving around and interact with each other.
Then, I
cannot do NVT or NPT equilibration.
Could you please let me know how can I control this kind of movements?


If molecules that should be restrained are moving inappropriately, then the
restraints are not being replied properly in the topology.  In the absence
of more substantial information, there's nothing else that can be said.

-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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--


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] Position Restraints

2012-04-26 Thread Dariush Mohammadyani

Thanks dear Justin.

No, the protein is moving in right direction, but I am going to restrain
any changing the position and then monitory these movements during MD run.
I could see the Pos. Res. works in md.log file.

Regards,
Dariush

On Thu, Apr 26, 2012 at 1:38 PM, Justin A. Lemkul  wrote:

>
>
> On 4/26/12 1:35 PM, Dariush Mohammadyani wrote:
>
>> Dear All,
>> I am using CG-MD using MARTINI forcefield. The system contains Protein
>> and lipid
>> bilayer. Although I used:
>> define = -DPOSRES
>> components in system were moving around and interact with each other.
>> Then, I
>> cannot do NVT or NPT equilibration.
>> Could you please let me know how can I control this kind of movements?
>>
>
> If molecules that should be restrained are moving inappropriately, then
> the restraints are not being replied properly in the topology.  In the
> absence of more substantial information, there's nothing else that can be
> said.
>
> -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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Re: [gmx-users] Position Restraints

2012-04-26 Thread Justin A. Lemkul




On 4/26/12 1:35 PM, Dariush Mohammadyani wrote:

Dear All,
I am using CG-MD using MARTINI forcefield. The system contains Protein and lipid
bilayer. Although I used:
define = -DPOSRES
components in system were moving around and interact with each other. Then, I
cannot do NVT or NPT equilibration.
Could you please let me know how can I control this kind of movements?


If molecules that should be restrained are moving inappropriately, then the 
restraints are not being replied properly in the topology.  In the absence of 
more substantial information, there's nothing else that can be said.


-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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Re: [gmx-users] Position restraints problem

2012-03-30 Thread Tsjerk Wassenaar

Hey :)

A sed oneliner to generate position_restraints for the first
moleculetype in a file, using an fc of 200:

sed -n -e '/\[ *atoms *\]/,/^ *\[/{/^\( *[0-9]\+\) .*/s//\1 1 200 200
200/p}' -e '/\[ *atoms *\]/i[ position_restraints ]' molecule.itp

Cheers,


Tsjerk


On Wed, Mar 28, 2012 at 3:33 PM, Jernej Zidar  wrote:
> True. Even more so if the position restraints file can be generated with 
> basic Bash commands in under a minute.
>
> Jernej
>
> On 28. mar. 2012, at 20:16, gmx-users-requ...@gromacs.org wrote:
>
>> It's pretty rare to have more than a handful of [moleculetype] sections,
>> each of which would want customized [position_restraints]. pdb2gmx will
>> write all-heavy-atom [position_restraints] sections which serve most
>> purposes. It would not be hard to modify genrestr to be useful in the
>> general case, but until a developer needs it badly enough, it'll be a
>> low priority :-)
>>
>> Mark
>
>
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] Position restraints problem

2012-03-28 Thread Jernej Zidar

True. Even more so if the position restraints file can be generated with basic 
Bash commands in under a minute.

Jernej

On 28. mar. 2012, at 20:16, gmx-users-requ...@gromacs.org wrote:

> It's pretty rare to have more than a handful of [moleculetype] sections, 
> each of which would want customized [position_restraints]. pdb2gmx will 
> write all-heavy-atom [position_restraints] sections which serve most 
> purposes. It would not be hard to modify genrestr to be useful in the 
> general case, but until a developer needs it badly enough, it'll be a 
> low priority :-)
> 
> Mark



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Re: [gmx-users] Position restraints problem

2012-03-28 Thread Mark Abraham


On 28/03/2012 7:39 PM, Jernej Zidar wrote:

On Wed, Mar 28, 2012 at 16:17,  wrote:

See the warning in genrestr -h.

If all you're doing is adding a single atom of position restraint per
moleculetype, you can do that by hand faster than using make_ndx and
genrestr and adding the #include.

Mark

This in turn means genrestr is useless if one has more than one
molecule type. While I could set the restraints manually,
doing it by hand is not really an option if one has more than 100
entries. Ah well, bash magic to the rescue.


It's pretty rare to have more than a handful of [moleculetype] sections, 
each of which would want customized [position_restraints]. pdb2gmx will 
write all-heavy-atom [position_restraints] sections which serve most 
purposes. It would not be hard to modify genrestr to be useful in the 
general case, but until a developer needs it badly enough, it'll be a 
low priority :-)


Mark



Thanks,
Jernej Zidar

For posterity reasons here's the warning:
WARNING: position restraints only work for the one molecule at a time.
Position restraints are interactions within molecules, therefore they should
be included within the correct [ moleculetype ] block in the topology. Since
the atom numbers in every moleculetype in the topology start at 1 and the
numbers in the input file for genrestr number consecutively from 1, genrestr
will only produce a useful file for the first molecule.


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Re: [gmx-users] Position restraints problem

2012-03-28 Thread Mark Abraham


On 28/03/2012 6:52 PM, Jernej Zidar wrote:

Hi.
   After successfully importing a CHARMM-generated PDB file to GROMACS
I set out to do some short simulations. While all calculations
finished without a problem if everything but the water molecules were
fixed.

   Removing the position restraints led to the system blowing up. Using
J. Lemkul's tutorial suggestion I generated an index file selecting
one lipid atom from sphingomyelin and one from cholesterol using
make_ndx and the selection: a P | a O3 (alternatively I tried also "6
| 7 | 17 | 18 | a P | a O3"). Any of the two selections selects only
atoms from the lipid part of the system.

   After creating the index file I used genrestr to position restrain
the movements of the selected atoms and obtain a position restrain ITP
file. I included this ITP file at the end of the lipid topology ITP
file as instructed on GROMACS' website.

  In the last step I edited the MDP file to use the position restraints
file for some lipid atoms but something went wrong as GROMPP
complains:
Fatal error:
[ file sys9-tmp-ions-mini-nofix-2-posre.itp, line 116 ]:
Atom index (12014) in position_restraints out of bounds (1-11954).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

   Indeed, checking the lipid ITP file revealed there is no atom index
12014, yet there is an atom index 12014 (with the proper name) in the
GRO file (that I used to create both the index and the restraints
file) where all the atoms are listed. What have I done wrong?


See the warning in genrestr -h.

If all you're doing is adding a single atom of position restraint per 
moleculetype, you can do that by hand faster than using make_ndx and 
genrestr and adding the #include.


Mark
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Re: [gmx-users] position restraints on heavy atoms or all?

2011-10-31 Thread Mark Abraham


On 30/10/2011 11:04 AM, Yun Shi wrote:

Hello all,

I am using amber99SB to model an antibody with organic ligands.

I know we could choose to restrain all atoms or only heavy atoms 
during the equilibration. But I wonder if this really matters for my 
system. As far as I know, equilibration is aimed at getting the 
temperature and pressure right, mainly for the solvent. And as long as 
we are going to do a 'real' MD production run without restraints, it 
should not matter too much how we restrained the antibody and ligands?


Initial velocities are sampled from a theoretical distribution. Initial 
positions can be quite unphysical from whatever process created them - 
particularly hydrogen atoms. These can combine poorly in the absence of 
some sensible restraints. Only you can assess the quality of your input 
model.


Mark



I am not if I am right about this. Any suggestions?

Thanks,
Yun




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Re: [gmx-users] Position restraints with multiple identical molecules

2011-06-16 Thread Craig Kitchen

Hi Justin, 

Ok - the .tpr file only lists the atoms from the molecule type. I get it 
now. Thanks again!


Craig



On 16 Jun 2011, at 12:58, Justin A. Lemkul wrote:



Craig Kitchen wrote: Dear All, My system consists of 32 identical molecules 
(with 91 atoms per molecule). I would like to apply a position restraint to 
the 91st atom of each molecules. Since all my molecules are identical I 
only have one [moleculetype] which contains 91 atoms. I have defined 
-DPOSRES in the .mdp file and have placed: #ifdef POSRES #include 
"posre.itp" #endif in (hopefully) the correct part of the topology file 
(immediately below the only [moleculetype]). There are no solvent molecules 
or ions. Applying a position restraint to atom 91 works fine with posre.itp 
containing: [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 
2000 2000 This results in just one restraint to atom 91. But if I want to 
restrain the 91st atom in the second molecule (atom 182 in the .gro file), 
how do I do it?


You already are. The [position_restraints] directive is applied to the 
atom(s) of the [moleculetype] that contains it, so if you only have one 
[moleculetype] then any instance of it will have the restraint applied to 
whatever atoms are indicated.


-Justin

[ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000 
182 1 2000 2000 2000 Does not work since 182 is outside the atom numbers in 
the [moleculetype] (1 to 91). Similarly, having 32 lines in posre.itp 
reading "91 1 2000 2000 2000" gives 32 position restraints to atom 91. I 
expect I can get around this problem by duplicating the current topology 32 
times and creating a huge topol.top file with all 2912 atoms defined 
explicitly. However, it seems there should be a more elegant way to achieve 
this. Any help would be greatly appreciated! I have included below a 
simplified example with all the other atoms removed. In this case, how do 
you restrain the position of atom 2,3,4 and 5? Craig Craig Kitchen 
Department of Chemistry University of Cambridge Lensfield Road Cambridge 
CB2 1EW UK topol.top: [ moleculetype ] ; Atom ; Name nrexcl UNK 3 [ atoms ] 
; nr type resnr resid atom cgnr charge mass

  1   amber99_41 1  UNK OAI 1   -0.50762  15.9994
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
[ system ]
; Name
Multiple Atoms
[ molecules ]
; Compound#mols
UNK   5
Starting conf.gro:
Multiple Atoms
5
 1UNKOAI1   0.767   1.527   0.970
 2UNKOAI2   0.988   0.716   1.774
 3UNKOAI3   0.556   0.587   0.434
 4UNKOAI4   0.335   1.656   2.436
 5UNKOAI5   0.766   1.527   2.373
2.64620   3.76260   2.80720
File used for restraint coordinates (grompp -r) :
Restraint coordinates
 5
 1UNKOAI1   0.000   1.500   1.000
 2UNKOAI2   1.100   0.621   2.000
 3UNKOAI3   0.399   0.621   0.349
 4UNKOAI4   0.221   1.562  -0.343
 5UNKOAI5   0.923   1.561   2.458
2.64620   3.76260   2.80720

--


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] Position restraints with multiple identical molecules

2011-06-16 Thread Craig Kitchen

You already are. The [position_restraints] directive is applied to the 
atom(s) of the [moleculetype] that >contains it, so if you only have one 
[moleculetype] then any instance of it will have the restraint >applied 
to whatever atoms are indicated.


-Justin


Hi Justin, thanks for your reply. 

If this is the case then should I not expect to see all the position 
restraints in the .tpr file?


Using gmxdump -s md1.tpr to inspect the file I can only see

Position Rest.:
nr: 2
iatoms:
   0 type=1 (POSRES) 0

(this is on the simplified 5 atom case). Which implies there is one 
position restraint on atom 1 (index 0 I guess).


Craig

Craig Kitchen wrote: Dear All, My system consists of 32 identical molecules 
(with 91 atoms per molecule). I would like to apply a position restraint to 
the 91st atom of each molecules. Since all my molecules are identical I 
only have one [moleculetype] which contains 91 atoms. I have defined 
-DPOSRES in the .mdp file and have placed: #ifdef POSRES #include 
"posre.itp" #endif in (hopefully) the correct part of the topology file 
(immediately below the only [moleculetype]). There are no solvent molecules 
or ions. Applying a position restraint to atom 91 works fine with posre.itp 
containing: [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 
2000 2000 This results in just one restraint to atom 91. But if I want to 
restrain the 91st atom in the second molecule (atom 182 in the .gro file), 
how do I do it?


You already are. The [position_restraints] directive is applied to the 
atom(s) of the [moleculetype] that contains it, so if you only have one 
[moleculetype] then any instance of it will have the restraint applied to 
whatever atoms are indicated.


-Justin

[ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000 
182 1 2000 2000 2000 Does not work since 182 is outside the atom numbers in 
the [moleculetype] (1 to 91). Similarly, having 32 lines in posre.itp 
reading "91 1 2000 2000 2000" gives 32 position restraints to atom 91. I 
expect I can get around this problem by duplicating the current topology 32 
times and creating a huge topol.top file with all 2912 atoms defined 
explicitly. However, it seems there should be a more elegant way to achieve 
this. Any help would be greatly appreciated! I have included below a 
simplified example with all the other atoms removed. In this case, how do 
you restrain the position of atom 2,3,4 and 5? Craig Craig Kitchen 
Department of Chemistry University of Cambridge Lensfield Road Cambridge 
CB2 1EW UK topol.top: [ moleculetype ] ; Atom ; Name nrexcl UNK 3 [ atoms ] 
; nr type resnr resid atom cgnr charge mass

  1   amber99_41 1  UNK OAI 1   -0.50762  15.9994
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
[ system ]
; Name
Multiple Atoms
[ molecules ]
; Compound#mols
UNK   5
Starting conf.gro:
Multiple Atoms
5
 1UNKOAI1   0.767   1.527   0.970
 2UNKOAI2   0.988   0.716   1.774
 3UNKOAI3   0.556   0.587   0.434
 4UNKOAI4   0.335   1.656   2.436
 5UNKOAI5   0.766   1.527   2.373
2.64620   3.76260   2.80720
File used for restraint coordinates (grompp -r) :
Restraint coordinates
 5
 1UNKOAI1   0.000   1.500   1.000
 2UNKOAI2   1.100   0.621   2.000
 3UNKOAI3   0.399   0.621   0.349
 4UNKOAI4   0.221   1.562  -0.343
 5UNKOAI5   0.923   1.561   2.458
2.64620   3.76260   2.80720

--


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] Position restraints with multiple identical molecules

2011-06-16 Thread Justin A. Lemkul




Craig Kitchen wrote:

Dear All,
My system consists of 32 identical molecules (with 91 atoms per 
molecule). I would like to apply a position restraint to the 91st atom 
of each molecules. Since all my molecules are identical I only have one 
[moleculetype] which contains 91 atoms. I have defined -DPOSRES in the 
.mdp file and have placed:


#ifdef POSRES
#include "posre.itp"
#endif

in (hopefully) the correct part of the topology file (immediately below 
the only [moleculetype]). There are no solvent molecules or ions.


Applying a position restraint to atom 91 works fine with posre.itp 
containing:


[ position_restraints ]
; ai funct fc (in x, y and z)
91 1 2000 2000 2000

This results in just one restraint to atom 91. But if I want to restrain 
the 91st atom in the second molecule (atom 182 in the .gro file), how do 
I do it?




You already are.  The [position_restraints] directive is applied to the atom(s) 
of the [moleculetype] that contains it, so if you only have one [moleculetype] 
then any instance of it will have the restraint applied to whatever atoms are 
indicated.


-Justin


[ position_restraints ]
; ai funct fc (in x, y and z)
91 1 2000 2000 2000
182 1 2000 2000 2000

Does not work since 182 is outside the atom numbers in the 
[moleculetype] (1 to 91). Similarly, having 32 lines in posre.itp 
reading "91 1 2000 2000 2000" gives 32 position restraints to atom 91.


I expect I can get around this problem by duplicating the current 
topology 32 times and creating a huge topol.top file with all 2912 atoms 
defined explicitly. However, it seems there should be a more elegant way 
to achieve this. Any help would be greatly appreciated!


I have included below a simplified example with all the other atoms 
removed. In this case, how do you restrain the position of atom 2,3,4 
and 5?


Craig

Craig Kitchen
Department of Chemistry
University of Cambridge
Lensfield Road
Cambridge
CB2 1EW
UK

topol.top:

[ moleculetype ]
; Atom
; Name nrexcl
UNK3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
1   amber99_41 1  UNK OAI 1   -0.50762  15.9994

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

[ system ]
; Name
Multiple Atoms

[ molecules ]
; Compound#mols
UNK   5

Starting conf.gro:

Multiple Atoms
5
   1UNKOAI1   0.767   1.527   0.970
   2UNKOAI2   0.988   0.716   1.774
   3UNKOAI3   0.556   0.587   0.434
   4UNKOAI4   0.335   1.656   2.436
   5UNKOAI5   0.766   1.527   2.373
  2.64620   3.76260   2.80720

File used for restraint coordinates (grompp -r) :

Restraint coordinates
   5
   1UNKOAI1   0.000   1.500   1.000
   2UNKOAI2   1.100   0.621   2.000
   3UNKOAI3   0.399   0.621   0.349
   4UNKOAI4   0.221   1.562  -0.343
   5UNKOAI5   0.923   1.561   2.458
  2.64620   3.76260   2.80720



--


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] Position restraints

2011-06-16 Thread Mark Abraham


On 16/06/2011 11:54 AM, Tom Dupree wrote:

Greetings all,

I have run into a little bit of a problem.

I am trying to simulate a hetro-dimer. Through previous work we have identified 
302  C-alphas (of 960 odd residues) that don't move much. Previously we 
position restrained these atoms in our simulations using charmm which gave us a 
significant speed up in simulation time. My supervisor is keen for me to do a 
comparison of that method with a completely unrestrained system using the 53A6 
FF. I managed to generate a position restraint file using the .gro file and 
genrestr.
However when I get to the simulation step I can't get grompp to work.


As genrestr -h will warn you, its output is only useful for the first 
molecule.


GROMACS position restraints will not give you any implementation-related 
speed-up, only one from reducing the sampling volume. Freeze groups will 
give you some speed-up (at the cost of making your results depend on 
your frozen configuration), but you will usually not be able to use both 
constraints and NPT as well.



I ran

genrestr -f em.gro -n subset.ndx -o subset.itp -disre -constr


Such a constraint or distance restraint matrix can only work 
intra-[moleculetype], and so is futile for your case.



As I understand my situation grompp is looking for atom numbers in subset.itp 
and matching them to the atom numbers in topol_Protein_chain_x.itp and since 
the atom numbers in subset.itp are based on the em.gro file it fails/goes out 
of range.


Yep


Thanks to some chain breaks in my structure I have 6 chains instead of 2, is 
there a way convert the .gro numbers into the .itp numbers? and hence generate 
my restraint files based on the topol_Protein_chain_x.itp files?


Sure, use editconf with some appropriate index groups (and maybe -resnr) 
to create subset structures that will then produce output from genrestr 
suitable for use with grompp.



   Furthermore can I actually do a constraint matrix over multiple molecules?


Not without uniting the [moleculetypes]. Do note that the various kinds 
of restraints, constraints and freeze groups are all distinct 
approaches, and attempting to mix them can be asking for trouble. Be 
sure to use the right terminology when asking for help :-)


Mark


Or is there a better way of achieving my desired result? (302 atoms across 2 
(6) chains constrained in their relative positions)


All the best,

Tom


Fatal error:
[ file subset.itp, line 145 ]:
Atom index (5222) in constraints out of bounds (1-5149).
This probably means that you have inserted topology section "constraints"
in a part belonging to a different molecule than you intended to.
In that case move the "constraints" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

My topology file
;
;   File 'topol.top' was generated
;   By user: onbekend (0)
;   On host: onbekend
;   At date: Tue May 31 11:44:23 2011
;
;   This is a standalone topology file
;
;   It was generated using program:
;   pdb2gmx - VERSION 4.5.3
;
;   Command line was:
;   pdb2gmx -f 3LP2.pdb -o 3lp2 -ignh -v
;
;   Force field was read from the standard Gromacs share directory.
;

; Include forcefield parameters
#include "gromos53a6.ff/forcefield.itp"

; Include chain topologies
#include "topol_Protein_chain_A.itp"
#ifdef POSRES
#include "posre_Protein_chain_A.itp"
#endif
#include "topol_Protein_chain_A2.itp"
#ifdef POSRES
#include "posre_Protein_chain_A2.itp"
#endif
#ifdef REST
#include "subset.itp"
#endif
#include "topol_Protein_chain_B.itp"
#ifdef POSRES
#include "posre_Protein_chain_B.itp"
#endif
#ifdef REST
#include "subset.itp"
#endif
#include "topol_Protein_chain_B2.itp"
#ifdef POSRES
#include "posre_Protein_chain_B2.itp"
#endif
#ifdef REST
#include "subset.itp"
#endif
#include "topol_Protein_chain_B3.itp"
#ifdef POSRES
#include "posre_Protein_chain_B3.itp"
#endif
#ifdef REST
#include "subset.itp"
#endif
#include "topol_Protein_chain_B4.itp"
#ifdef POSRES
#include "posre_Protein_chain_B4.itp"
#endif
#ifdef REST
#include "subset.itp"
#endif
___




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Re: [gmx-users] Position restraints

2011-04-09 Thread Justin A. Lemkul




Mikhail Stukan wrote:

Dear gmx-users,

 

I am trying to simulate a thermalized wall in the framework of CG 
Martini force field. To do this I am planning to link my wall atoms to 
some reference points (initial positions) by harmonic potentials. From 
what I have found in the manual it looks like this can be done by using 
[position_restraints] declaration. What is not clear to me from the 
manual is if I understand correctly that as the “reference position” 
GROMACS will use the initial positions of the particles mentioned in 
[position_restraints] decraration? If yes then which positions of the 


Correct.

wall particles will be written out at the end of the run? The initial 
ones (“reference positions”) or the instantaneous position of these 
particle at the end of the run?


 


The instantaneous positions.  Since the atoms can move using position restraints 
(with the amount controlled by the force constant specified), there is no 
guarantee that the positions will not change, and in fact, they usually do, even 
if the amount is very small.


-Justin



Many thanks in advance,

Mikhail

 


=

Dr Mikhail Stukan

Schlumberger Dhahran Carbonate Research Center,

Dhahran Techno Valley  - KFUPM,

P.O. Box 39011, Dammam / Doha Camp  31942,

Kingdom of Saudi Arabia

Tel: +966 3 331 6182

Fax:+966 3 330 0845
mstu...@slb.com 

 



--


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] position restraints and out of bounds atom index

2010-10-18 Thread Alexandre Suman de Araujo

Since anybody helped me with this issue and I solved the problem, I'll 
report the solution here to contribute with the comunity.


As I pointed in the original e-mail, the problem was the difference 
between the numbering scheme of .gro file and .itp file.


I created 3 .pdb files, one for each chain and with pdb2gmx I created 3 
.gro files. With these 3 .gro files I created 3 .ndx files with the 
groups I'd like to apply PR and from these .ndx files I created the PR 
.itp files, now with the numbering agreeing with the one of the topology 
files.
The include of these PR.itp files in .top file is the same I mentioned 
in the original e-mail.


With this, everything worked fine.

Cheers

**
Alexandre Suman de Araujo*
Faculdade de Ciências Farmacêuticas de Ribeirão Preto*
Universidade de São Paulo*
Dep. de Física e Química *
Grupo de Física Biológica * e-mail: asara...@fcfrp.usp.br*
Av. do Café, s/n° * e-mail: ale.su...@gmail.com  *
CEP: 14040-903* Phone: +55 (16) 3602-4172*
Ribeirão Preto, SP, Brasil* Phone: +55 (16) 3602-4222*
**


Em 16-10-2010 15:41, Alexandre Suman de Araujo escreveu:

Hi all

I'm trying to simulate a system with 3 chains (A, H and L).

Pb2gmx gave me 3 .itp files (one for each chain), each one with atom 
number starting from 1, and a .top file with these 3 .itp included. It 
gave me also a .gro file with the 3 chains numbered consecutively (the 
atom number does not restart from 1 for each chain).


With this .gro file I made an index file using make_ndx with 3 groups 
containing the backbone of each chain. With this index file I built 3 
position restraint files with genrestr, one for each chain.


Following the instructions from website, I removed the #ifdef 
POSRES/#include/#endif lines from the end of the .itp file of each 
chain and added them directly in the .top file as shown below:



;
;File 'proteina.gro.top' was generated
;By user: onbekend (0)
;On host: onbekend
;At date: Thu Oct 14 14:22:01 2010
;
;This is a standalone topology file
;
;It was generated using program:
;pdb2gmx - VERSION 4.5.1
;
;Command line was:
;pdb2gmx -f 2R29CL_original.pdb -o protein.gro -p proteina.gro 
-his -ignh

;
;Force field was read from the standard Gromacs share directory.
;

; Include forcefield parameters
#include "oplsaa.ff/forcefield.itp"

; Include chain topologies
#include "proteina.gro_Protein_chain_A.itp"
; Include Position restraint file for chain A
#ifdef POSRES
#include "posre_Protein_chain_A.itp"
#endif

#include "proteina.gro_Protein_chain_H.itp"
; Include Position restraint file for chain H
#ifdef POSRES
#include "posre_Protein_chain_H.itp"
#endif

#include "proteina.gro_Protein_chain_L.itp"
; Include Position restraint file for chain L
#ifdef POSRES
#include "posre_Protein_chain_L.itp"
#endif

; Include water topology
#include "oplsaa.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include topology for ions
#include "oplsaa.ff/ions.itp"

[ system ]
; Name
ENVELOPE PROTEIN E; HEAVY CHAIN OF FAB 1A1D-2; LIGHT CHAIN OF FAB 
1A1D-2 in water


[ molecules ]
; Compound#mols
Protein_chain_A 1
Protein_chain_H 1
Protein_chain_L 1
SOL59
SOL97
SOL95
SOL 30308
NA  91
CL  97


When I run a simulation without the "define = -DPOSRES" definition in 
the .mdp file, grompp runs ok. However, when I say in .mdp file to use 
position restraints grompp give me the following error:


Fatal error:
[ file posre_Protein_chain_H.itp, line 334 ]:
Atom index (3221) in position_restraints out of bounds (1-3212).
This probably means that you have inserted topology section 
"position_restraints"

in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right 
molecule.
For more information and tips for troubleshooting, please check the 
GROMACS

website at http://www.gromacs.org/Documentation/Errors

I know that this was already discussed in list but nothing described 
there worked.


It is clear that the problem is due to the different numbering scheme 
of the .gro file and .itp files. The .gro file does not restart the 
numbering scheme when a new chain starts, on the other hand, the .itp 
file of each chain starts from 1 in atom number field. Since the 
position restraint file is generated based on numbering scheme of the 
.gro file, in some cases (my case is one of them) the PR file refers 
to a atom number that does not exists in .itp file.


I think the way to correct this was generate

RE: [gmx-users] Position Restraints

2010-09-21 Thread #ZHAO LINA#

Thanks for your answer again.

I will restrain the heavy atoms only first.

Best regards,

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Wednesday, September 22, 2010 11:43 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Position Restraints

#ZHAO LINA# wrote:
> Thanks for your answer.
>
> How can I tell which ones I should restrain? all no-H atoms? in most general 
> situations.

For the sake of clarity in the archive, it's probably best to avoid broad
generalizations.  People can easily stumble upon a post and take it way out of
context.  A "general situation" might encompass a lot.  I will reiterate that if
you want to recapitulate the behavior of pdb2gmx with respect to typical
biomolecules, you should choose all non-H atoms.

If you have some other specialized application, I can make no recommendation,
nor can anyone else, in the absence of a more thorough description.

-Justin

>
> lina
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
> of Justin A. Lemkul [jalem...@vt.edu]
> Sent: Wednesday, September 22, 2010 11:15 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Position Restraints
>
> #ZHAO LINA# wrote:
>>  Hi,
>>
>> When I used the genrestr to get the posre.itp specially,
>> I found it set all atom to be applied to.
>> Is that okay? How could I figure out which ones should not be set to.
>>
>> A little naive questions, but I do do not know.
>
> The answer depends on your needs.  When running genrestr without an index 
> file,
> you can choose from any of the default groups.  If you provide an index file,
> any group can be chosen.
>
> The default behavior of pdb2gmx is to generate a posre.itp file that restrains
> all heavy (non-H) atoms.  You can do the same with genrestr if you want, but
> again, the atoms you want to restrain depend on your goals.
>
> -Justin
>
>> Thanks with regards,
>>
>> lina
>>
>
> --
> 
>
> 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/Support/Mailing_Lists/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/Support/Mailing_Lists

--


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] Position Restraints

2010-09-21 Thread Justin A. Lemkul




#ZHAO LINA# wrote:

Thanks for your answer.

How can I tell which ones I should restrain? all no-H atoms? in most general 
situations.


For the sake of clarity in the archive, it's probably best to avoid broad 
generalizations.  People can easily stumble upon a post and take it way out of 
context.  A "general situation" might encompass a lot.  I will reiterate that if 
you want to recapitulate the behavior of pdb2gmx with respect to typical 
biomolecules, you should choose all non-H atoms.


If you have some other specialized application, I can make no recommendation, 
nor can anyone else, in the absence of a more thorough description.


-Justin



lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Wednesday, September 22, 2010 11:15 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Position Restraints

#ZHAO LINA# wrote:

 Hi,

When I used the genrestr to get the posre.itp specially,
I found it set all atom to be applied to.
Is that okay? How could I figure out which ones should not be set to.

A little naive questions, but I do do not know.


The answer depends on your needs.  When running genrestr without an index file,
you can choose from any of the default groups.  If you provide an index file,
any group can be chosen.

The default behavior of pdb2gmx is to generate a posre.itp file that restrains
all heavy (non-H) atoms.  You can do the same with genrestr if you want, but
again, the atoms you want to restrain depend on your goals.

-Justin


Thanks with regards,

lina



--


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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--


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] Position Restraints

2010-09-21 Thread #ZHAO LINA#

Thanks for your answer.

How can I tell which ones I should restrain? all no-H atoms? in most general 
situations.

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Wednesday, September 22, 2010 11:15 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Position Restraints

#ZHAO LINA# wrote:
>  Hi,
>
> When I used the genrestr to get the posre.itp specially,
> I found it set all atom to be applied to.
> Is that okay? How could I figure out which ones should not be set to.
>
> A little naive questions, but I do do not know.

The answer depends on your needs.  When running genrestr without an index file,
you can choose from any of the default groups.  If you provide an index file,
any group can be chosen.

The default behavior of pdb2gmx is to generate a posre.itp file that restrains
all heavy (non-H) atoms.  You can do the same with genrestr if you want, but
again, the atoms you want to restrain depend on your goals.

-Justin

>
> Thanks with regards,
>
> lina
>

--

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] Position Restraints

2010-09-21 Thread Justin A. Lemkul




#ZHAO LINA# wrote:

 Hi,

When I used the genrestr to get the posre.itp specially,
I found it set all atom to be applied to.
Is that okay? How could I figure out which ones should not be set to.

A little naive questions, but I do do not know.


The answer depends on your needs.  When running genrestr without an index file, 
you can choose from any of the default groups.  If you provide an index file, 
any group can be chosen.


The default behavior of pdb2gmx is to generate a posre.itp file that restrains 
all heavy (non-H) atoms.  You can do the same with genrestr if you want, but 
again, the atoms you want to restrain depend on your goals.


-Justin



Thanks with regards,

lina



--


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] position restraints

Have you seen the example here?

http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_defaults

What you need to do is place your [position_restraints] directive after the 
moleculetype to which it belongs, but before any other moleculetype has been 
introduced (usually by #including another topology, which introduces a new 
molecule, and hence, moleculetype).

The example I mentioned regarding posre.itp is to demonstrate exactly how this 
is done.  The posre.itp file is produced by pdb2gmx and is used to restrain the 
heavy atoms of the protein.  It is #included (basically inserting the relevant 
[position_restraints] directive) at the end of the Protein_A moleculetype 
definition, but prior to the #include "spc.itp" statement, which starts the SPC 
water moleculetype definition.

So the topology is like this:

[ moleculetype ]
Protein

(atoms, bonds, other stuff...)

[ position_restraints ] <- Note how it is placed before the next moleculetype.

[ moleculetype ] <- This part comes from the #include "spc.itp" statement.
SOL

etc.

-Justin

abdullah ahmed wrote:

Hi,

Sorry to bother you again, but I am new to gromacs and many theings 
don't make sense yet.
I have tried reading the manual but I do not understand what you mean by 
"Note how the automatically-generated "posre.itp" file is #included at 
the end of the Protein_A moleculetype, *before* any other molecules are 
introduced. You have to do the same with any new #include statements or 
directives you add."

I tried using #include in front of my code for [position_restraints] but 
that just gives an error. So I suppose that isn't what you mean.
Furthermore, in section 5.7.1 of the manual pg110 an example topology 
file called urea.top is shown. there is no include there.

In this example .top file they just seem to have added the position 
restraints they want after the dihedrals. This approach does not seem to 
be working for me and I can not understand why.

Thank you again for your help,
Abdullah

 > Date: Thu, 3 Jun 2010 09:43:18 -0400
 > From: jalem...@vt.edu
 > To: gmx-users@gromacs.org
 > Subject: Re: [gmx-users] position restraints
 >
 >
 >
 > abdullah ahmed wrote:
 > > Hi!
 > >
 > > In your previous mail you mentioned:
 > >
 > > The position restraints must belong to the [moleculetype] of
 > > the species to be restrained. * Once you #include a new molecule, you
 > > start a new
 > > [moleculetype] entry and the position restraints belong to it. *
 > >
 > >
 > > So I rechecked my .top file and found that [moleculetype] only occurs
 > > once. Perhaps I have misunderstood you. So I added the top file 
below. I

 >
 > No it doesn't. Each time you #include a new .itp file, you are 
telling grompp
 > to copy and paste the contents of that .itp file in that location. 
Have a look

 > at spc.itp - it starts a new moleculetype.
 >
 > http://www.gromacs.org/Documentation/Include_File_Mechanism
 >
 > Note how the automatically-generated "posre.itp" file is #included at 
the end of
 > the Protein_A moleculetype, *before* any other molecules are 
introduced. You
 > have to do the same with any new #include statements or directives 
you add.

 >
 > -Justin
 >
 > > did not add the contents of [atoms] [bonds] etc because I felt the 
mail

 > > would become unnecessarily long.
 > >
 > > ; Include forcefield parameters
 > > #include "ffoplsaa.itp"
 > >
 > > [ moleculetype ]
 > > ; Name nrexcl
 > > Protein_A 3
 > >
 > > [ atoms ]
 > >
 > > [ bonds ]
 > >
 > > [ pairs ]
 > >
 > > [ angles ]
 > >
 > > [ dihedrals ]
 > >
 > > [ dihedrals ]
 > >
 > > ; Include Position restraint file
 > > #ifdef POSRES
 > > #include "posre.itp"
 > > #endif
 > >
 > > ; Include water topology
 > > #include "spc.itp"
 > >
 > > #ifdef POSRES_WATER
 > > ; Position restraint for each water oxygen
 > > [ position_restraints ]
 > > ; i funct fcx fcy fcz
 > > 1 1 1000 1000 1000
 > > #endif
 > >
 > > ; Include generic topology for ions
 > > #include "ions.itp"
 > >
 > > [ system ]
 > > ; Name
 > > Protein
 > >
 > > [ molecules ]
 > > ; Compound #mols
 > > Protein_A 1
 > >
 > > Thanks again for your help,
 > > Abdullah
 > >
 > >
 > > 

 > > Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign
 > > up now. <https://signup.live.com/signup.aspx?id=60969>
 >
 > --
 > ==

RE: [gmx-users] position restraints

2010-06-03 Thread abdullah ahmed

Hi,

Sorry to bother you again, but I am new to gromacs and many theings don't make 
sense yet. 
I have tried reading the manual but I do not understand what you mean by "Note 
how the automatically-generated "posre.itp" file is #included at 
the end of the Protein_A moleculetype, *before* any other 
molecules are introduced. You have to do the same with any new #include 
statements or 
directives you add." 

I tried using #include in front of my code for [position_restraints] but that 
just gives an error. So I suppose that isn't what you mean. 
Furthermore, in section 5.7.1 of the manual pg110 an example topology file 
called urea.top is shown. there is no include there.

In this example .top file they just seem to have added the position restraints 
they want after the dihedrals. This approach does not seem to be working for me 
and I can not understand why. 

Thank you again for your help, 
Abdullah

> Date: Thu, 3 Jun 2010 09:43:18 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] position restraints
> 
> 
> 
> abdullah ahmed wrote:
> > Hi!
> > 
> > In your previous mail you mentioned:
> > 
> > The position restraints must belong to the [moleculetype] of
> > the species to be restrained. * Once you #include a new molecule, you 
> > start a new
> > [moleculetype] entry and the position restraints belong to it. *
> >  
> > 
> > So I rechecked my .top file and found that [moleculetype] only occurs 
> > once. Perhaps I have misunderstood you. So I added the top file below. I 
> 
> No it doesn't.  Each time you #include a new .itp file, you are telling 
> grompp 
> to copy and paste the contents of that .itp file in that location.  Have a 
> look 
> at spc.itp - it starts a new moleculetype.
> 
> http://www.gromacs.org/Documentation/Include_File_Mechanism
> 
> Note how the automatically-generated "posre.itp" file is #included at the end 
> of 
> the Protein_A moleculetype, *before* any other molecules are introduced.  You 
> have to do the same with any new #include statements or directives you add.
> 
> -Justin
> 
> > did not add the contents of [atoms] [bonds] etc because I felt the mail 
> > would become unnecessarily long.
> > 
> > ; Include forcefield parameters
> > #include "ffoplsaa.itp"
> > 
> > [ moleculetype ]
> > ; Namenrexcl
> > Protein_A   3
> > 
> > [ atoms ]
> > 
> > [ bonds ]
> > 
> > [ pairs ]
> > 
> > [ angles ]
> > 
> > [ dihedrals ]
> > 
> > [ dihedrals ]
> > 
> > ; Include Position restraint file
> > #ifdef POSRES
> > #include "posre.itp"
> > #endif
> > 
> > ; Include water topology
> > #include "spc.itp"
> > 
> > #ifdef POSRES_WATER
> > ; Position restraint for each water oxygen
> > [ position_restraints ]
> > ;  i funct   fcxfcyfcz
> >11   1000   1000   1000
> > #endif
> > 
> > ; Include generic topology for ions
> > #include "ions.itp"
> > 
> > [ system ]
> > ; Name
> > Protein
> > 
> > [ molecules ]
> > ; Compound#mols
> > Protein_A   1
> > 
> > Thanks again for your help,
> > Abdullah
> > 
> > 
> > 
> > Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign 
> > up now. <https://signup.live.com/signup.aspx?id=60969>
> 
> -- 
> 
> 
> 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 
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Re: [gmx-users] position restraints




abdullah ahmed wrote:

Hi!

In your previous mail you mentioned:

The position restraints must belong to the [moleculetype] of
the species to be restrained. * Once you #include a new molecule, you 
start a new

[moleculetype] entry and the position restraints belong to it. *
 

So I rechecked my .top file and found that [moleculetype] only occurs 
once. Perhaps I have misunderstood you. So I added the top file below. I 


No it doesn't.  Each time you #include a new .itp file, you are telling grompp 
to copy and paste the contents of that .itp file in that location.  Have a look 
at spc.itp - it starts a new moleculetype.


http://www.gromacs.org/Documentation/Include_File_Mechanism

Note how the automatically-generated "posre.itp" file is #included at the end of 
the Protein_A moleculetype, *before* any other molecules are introduced.  You 
have to do the same with any new #include statements or directives you add.


-Justin

did not add the contents of [atoms] [bonds] etc because I felt the mail 
would become unnecessarily long.


; Include forcefield parameters
#include "ffoplsaa.itp"

[ moleculetype ]
; Namenrexcl
Protein_A   3

[ atoms ]

[ bonds ]

[ pairs ]

[ angles ]

[ dihedrals ]

[ dihedrals ]

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#include "spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein

[ molecules ]
; Compound#mols
Protein_A   1

Thanks again for your help,
Abdullah



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up 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] position restraints




abdullah ahmed wrote:

Thank you for your reply,

I have been using [ position_restraints ], I do not know why it came out 
that way in the mail.
I agree with you, the problem probably comes from the position the code 
lies in inside the .top file. I put it at the end of the file because I 
thought that was the way it was supposed to be done. Perhaps this is 
incorrect.




That is incorrect.  The position restraints must belong to the [moleculetype] of 
the species to be restrained.  Once you #include a new molecule, you start a new 
[moleculetype] entry and the position restraints belong to it.  Putting it at 
the very end of a file probably has no effect whatsoever on any of the species 
in your system.


-Justin


The final lines of the .top file are:

Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein

[ molecules ]
; Compound#mols
Protein_A   1

[ position_restraints ]
2 1 1000 0 1000 ;
3 1 1000 0 1000 ;
4 1 1000 0 1000 ;
5 1 1000 0 1000 ;
6 1 1000 0 1000 ;
7 1 1000 0 1000 ;
8 1 1000 0 1000 ;
9 1 1000 0 1000 ;

 


 > Date: Thu, 3 Jun 2010 09:00:36 -0400
 > From: jalem...@vt.edu
 > To: gmx-users@gromacs.org
 > Subject: Re: [gmx-users] position restraints
 >
 >
 >
 > abdullah ahmed wrote:
 > > Hello,
 > >
 > > I would like to restrain my molecule to a specific position in 
space. I

 > > would like for certain atoms to lie on the y-axis. To do this I used
 > > the following code/lines in my .top file:
 > >
 > > [ position restraints ]
 >
 > This is an incorrect directive. It should be position_restraints.
 >
 > > 2 1 1000 0 1000 ;
 > > 3 1 1000 0 1000 ;
 > > 4 1 1000 0 1000 ;
 > > 5 1 1000 0 1000 ;
 > > 6 1 1000 0 1000 ;
 > > 7 1 1000 0 1000 ;
 > > 8 1 1000 0 1000 ;
 > > 9 1 1000 0 1000 ;
 > >
 > > Unfortunately, after minimization my file contained the molecule in 
the

 > > same position as when the restraints were not applied.
 > >
 > > Does anyone know what I am doing wrong?
 > >
 >
 > Perhaps the directive name is an issue, although I think grompp 
should have
 > raised a warning of some sort. Otherwise, is this block within the 
appropriate
 > [moleculetype] in the topology? Is it under control of an #ifdef 
block that you

 > haven't invoked in the .mdp file?
 >
 > -Justin
 >
 > > Thanks in advance,
 > > Abdullah
 > >
 > > 


 > > Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up
 > > now. <https://signup.live.com/signup.aspx?id=60969>
 > >
 >
 > --
 > 
 >
 > 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 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. Get Windows Live Hotmail Free. Sign up 
now. <https://signup.live.com/signup.aspx?id=60969>


--


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] position restraints




abdullah ahmed wrote:

Hello,

I would like to restrain my molecule to a specific position in space. I 
would like for certain atoms to lie on the y-axis. To do this I used  
the following code/lines in my .top file:


[ position restraints ]


This is an incorrect directive.  It should be position_restraints.


2 1 1000 0 1000 ;
3 1 1000 0 1000 ;
4 1 1000 0 1000 ;
5 1 1000 0 1000 ;
6 1 1000 0 1000 ;
7 1 1000 0 1000 ;
8 1 1000 0 1000 ;
9 1 1000 0 1000 ;

Unfortunately, after minimization my file contained the molecule in the 
same position as when the restraints were not applied.


Does anyone know what I am doing wrong?



Perhaps the directive name is an issue, although I think grompp should have 
raised a warning of some sort.  Otherwise, is this block within the appropriate 
[moleculetype] in the topology?  Is it under control of an #ifdef block that you 
haven't invoked in the .mdp file?


-Justin


Thanks in advance,
Abdullah


Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up 
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] Position restraints on a pentamer

2008-08-15 Thread Justin A. Lemkul

[EMAIL PROTECTED] wrote:

Please ignore my previous mail. There was typo error.

Dear colleagues,

   I want to do MD simulation of only the extracellular 
domain of a pentamer, excluding the transmembrane domain. So, I want to 
restrain the part of the extracellular domain in contact with the 
transmembrane domain. I am using "position restraints" for few of those 
residues as well as to the two ends of one of the subunits, in which 
there are missing residues.

[ position_restraints ]
; atom  type  fx  fy  fz
   457 1  1000  1000  1000
   459 1  1000  1000  1000
   460 1  1000  1000  1000
   461 1  1000  1000  1000

 After few ns of MD, I observed that 3 of the subunits are distorted 
while the other 2 aren't.

Can you explain what you mean by distorted?  Or post images online somewhere?

1) Is this because of imposing position restraints or is it because of 
the gap in between (due to missing residues) in one of the subunits?

Potentially one or the other, or even both.  In science, we have to eliminate 
variables, so you may want to try one of two things (if not both, ultimately):

1. Remove position restraints.
2. Fix the missing residues in the model.

Depending on what you're interested in, either might be a viable option.  I 
would think you'd like to rebuild the missing residues, unless you think they 
will have absolutely no effect on the dynamics.

2)Is there any other way to restrain (apart from position restraints) 
the protein for this purpose?

There is an option within the .mdp file called freezegrps.  Note that this 
option doesn't work well when applying pressure coupling.

-Justin

Coming to the missing residues part, I decided to use distance 
restraints between the two ends. Please note that only one of the chain 
is in covalently linked with the transmembrane domain. Rest of them have 
vanderwaals interactions.

Thanks for any kind of suggestion in this regard.

Prema.

- Original Message -
From: <[EMAIL PROTECTED]>
Date: Friday, August 15, 2008 2:00 pm
Subject: Position restraints on a pentamer
To: gmx-users@gromacs.org

 > Dear colleagues,
 >
 >I want to do MD simulation of only the
 > extracellular domain of a pentamer, excluding the transmembrane
 > domain. So, I want to restrain the part of the extracellular
 > domain in contact with the transmembrane domain. I am using
 > "position restraints" for few of those residues as well as to
 > the two ends of one of the subunits, in which there are missing
 > residues.
 > [ position_restraints ]
 > ; atom  type  fx  fy  fz
 >457 1  1000  1000  1000
 >459 1  1000  1000  1000
 >460 1  1000  1000  1000
 >461 1  1000  1000  1000
 >
 >
 >  After few ns of MD, I observed that 3 of the subunits are
 > distorted while the other 2 aren't.
 >
 > 1) Is this because of imposing position restraints or is it
 > because of the gap between two subunits in on the subunits?
 >
 > 2)Is there any other way to restrain (apart from position
 > restraints) the protein for this purpose?
 >
 > Coming to the missing residues part, I decided to use
 > distance restraints between the two ends. Please note that only
 > one of the chain is in covalently linked with the transmembrane
 > domain. Rest of them have vanderwaals interactions.
 >
 > Thanks for any kind of suggestion in this regard.
 >
 > Prema.
 >
 >

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--

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Graduate Research Assistant
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] position restraints

Quoting [EMAIL PROTECTED]:

> Hi,
>
> I minimized without restraints, could that be the problem?
> After the minimization I got a Potential Energy  = -6.1434351e+02.

That seems fine.  Basically, your lipid's headgroup is shearing itself apart
(which you can tell from the LINCS warnings).  At this point, I could only
guess as to what's going wrong, which probably won't do you much good.

If you'd like to send me your structure, topologies, and .mdp file off-list, I'd
be happy to have a look at them.

-Justin

>
> Gadi
>
>
> Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>:
>
> > Quoting [EMAIL PROTECTED]:
> >
> >> Hi,
> >>
> >> The full mdrun output when the simulation blows up is:
> >>
> >> Step 0, time 0 (ps)  LINCS WARNING
> >> relative constraint deviation after LINCS:
> >> max inf (between atoms 6 and 7) rms inf
> >> bonds that rotated more than 30 degrees:
> >>   .
> >>   .
> >>   .
> >> Warning: 1-4 interaction between 1 and 6 at distance
> >> 324490777485109120.000 which is larger than the 1-4 table size 1.000 nm
> >> These are ignored for the rest of the simulation
> >> This usually means your system is exploding,
> >> if not, you should increase table-extension in your mdp file
> >
> > Basic information about this type of error can be found here (as
> > well as several
> > hundred posts in the list archive):
> >
> > http://wiki.gromacs.org/index.php/Errors#LINCS_warnings
> >
> > How did you do your minimization, with or without restraints?  Did
> > it converge
> > to an acceptable potential energy?
> >
> > -Justin
> >
> >>
> >> Thanks Gadi
> >>
> >> Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>:
> >>
> >> >
> >> > Did your minimization converge to a nice, negative potential energy?
> >> >   Also, what
> >> > is the full mdrun output when the simulation blows up?  You've
> >> > quoted the last
> >> > bit, but it would be more informative to see the whole output, or at
> least
> >> a
> >> > description of it (i.e., LINCS warnings).
> >> >
> >> > -Justin
> >> >
> >> > Quoting [EMAIL PROTECTED]:
> >> >
> >> >>
> >> >> Hi,
> >> >>
> >> >> I tried using no temperature coupling and no constraints, that did not
> >> help.
> >> >> If I run the simulation without the position restraints it works OK.
> >> >> Could there by something wrong with the posre file (I'll attach it at
> >> >> the end of the email).
> >> >> I want one of the atoms in the lipid to stay in one place and the rest
> >> >> to wiggle around it. Is there any other way to do that which is not
> >> >> position restraints.
> >> >>
> >> >> Thanks Gadi
> >> >>
> >> >>
> >> >> [ position_restraints ]
> >> >> ; atom  type  fx  fy  fz
> >> >>   1 1  0  0  0
> >> >>   2 1  0  0  0
> >> >>   3 1  0  0  0
> >> >>   4 1  0  0  0
> >> >>   5 1  0  0  0
> >> >>   6 1  0  0  0
> >> >>   7 1  0  0  0
> >> >>   8 1  1000.0  1000.0  1000.0
> >> >>   9 1  0  0  0
> >> >>  10 1  0  0  0
> >> >>  11 1  0  0  0
> >> >>  12 1  0  0  0
> >> >>  13 1  0  0  0
> >> >>  14 1  0  0  0
> >> >>  15 1  0  0  0
> >> >>  16 1  0  0  0
> >> >>  17 1  0  0  0
> >> >>  18 1  0  0  0
> >> >>  19 1  0  0  0
> >> >>  20 1  0  0  0
> >> >>  21 1  0  0  0
> >> >>  22 1  0  0  0
> >> >>  23 1  0  0  0
> >> >>  24 1  0  0  0
> >> >>  25 1  0  0  0
> >> >>  26 1  0  0  0
> >> >>  27 1  0  0  0
> >> >>  28 1  0  0  0
> >> >>  29 1  0  0  0
> >> >>  30 1  0  0  0
> >> >>  31 1  0  0  0
> >> >>  32 1  0  0  0
> >> >>  33 1  0  0  0
> >> >>  34 1  0  0  0
> >> >>  35 1  0  0  0
> >> >>  36 1  0  0  0
> >> >>  37 1  0  0  0
> >> >>  38 1  0  0  0
> >> >>  39 1  0  0  0
> >> >>  40 1  0  0  0
> >> >>  41 1  0  0  0
> >> >>  42 1  0  0  0
> >> >>  43 1  0  0  0
> >> >>  44 1  0  0  0
> >> >>  45 1  0  0  0
> >> >>  46 1  0  0  0
> >> >>  47 1  0  0  0
> >> >>  48 1  0  0  0
> >> >>  49 1  0  0  0
> >> >>  50 1  0  0  0
> >> >>
> >> >> Quoting Mark Abraham <[EMAIL PROTECTED]>:
> >> >>
> >> >> > [EMAIL PROTECTED] wrote:
> >> >> >
> >> >> > Please generate replies to the mailing list sensibly. It's very hard
> to
> >> >> > work out who you are quoting where in this email. It'd be easy just
> to
> >> >> > ignore it, and that's the last thing you should want.
> >> >> >
> >> >> >> Hello,
> >> >> >>
> >> >> >> I'm trying to run a simulation with one lipid molecule in a fixed
> >> >> >> simulation box without pbc.
> >> >> >> I set position restraints on one of the atoms and I seem to keep on
> >> >> >> getting the following error:
> >> >> >
> >> >> > Why do you want MD of a single lipid and a position restraint on one
> >> >> > atom? If you just want to see a lipid wiggl

Re: [gmx-users] position restraints


Hi,

I minimized without restraints, could that be the problem?
After the minimization I got a Potential Energy  = -6.1434351e+02.

Gadi


Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>:


Quoting [EMAIL PROTECTED]:


Hi,

The full mdrun output when the simulation blows up is:

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max inf (between atoms 6 and 7) rms inf
bonds that rotated more than 30 degrees:
  .
  .
  .
Warning: 1-4 interaction between 1 and 6 at distance
324490777485109120.000 which is larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file


Basic information about this type of error can be found here (as   
well as several

hundred posts in the list archive):

http://wiki.gromacs.org/index.php/Errors#LINCS_warnings

How did you do your minimization, with or without restraints?  Did   
it converge

to an acceptable potential energy?

-Justin



Thanks Gadi

Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>:

>
> Did your minimization converge to a nice, negative potential energy?
>   Also, what
> is the full mdrun output when the simulation blows up?  You've
> quoted the last
> bit, but it would be more informative to see the whole output, or at least
a
> description of it (i.e., LINCS warnings).
>
> -Justin
>
> Quoting [EMAIL PROTECTED]:
>
>>
>> Hi,
>>
>> I tried using no temperature coupling and no constraints, that did not
help.
>> If I run the simulation without the position restraints it works OK.
>> Could there by something wrong with the posre file (I'll attach it at
>> the end of the email).
>> I want one of the atoms in the lipid to stay in one place and the rest
>> to wiggle around it. Is there any other way to do that which is not
>> position restraints.
>>
>> Thanks Gadi
>>
>>
>> [ position_restraints ]
>> ; atom  type  fx  fy  fz
>>   1 1  0  0  0
>>   2 1  0  0  0
>>   3 1  0  0  0
>>   4 1  0  0  0
>>   5 1  0  0  0
>>   6 1  0  0  0
>>   7 1  0  0  0
>>   8 1  1000.0  1000.0  1000.0
>>   9 1  0  0  0
>>  10 1  0  0  0
>>  11 1  0  0  0
>>  12 1  0  0  0
>>  13 1  0  0  0
>>  14 1  0  0  0
>>  15 1  0  0  0
>>  16 1  0  0  0
>>  17 1  0  0  0
>>  18 1  0  0  0
>>  19 1  0  0  0
>>  20 1  0  0  0
>>  21 1  0  0  0
>>  22 1  0  0  0
>>  23 1  0  0  0
>>  24 1  0  0  0
>>  25 1  0  0  0
>>  26 1  0  0  0
>>  27 1  0  0  0
>>  28 1  0  0  0
>>  29 1  0  0  0
>>  30 1  0  0  0
>>  31 1  0  0  0
>>  32 1  0  0  0
>>  33 1  0  0  0
>>  34 1  0  0  0
>>  35 1  0  0  0
>>  36 1  0  0  0
>>  37 1  0  0  0
>>  38 1  0  0  0
>>  39 1  0  0  0
>>  40 1  0  0  0
>>  41 1  0  0  0
>>  42 1  0  0  0
>>  43 1  0  0  0
>>  44 1  0  0  0
>>  45 1  0  0  0
>>  46 1  0  0  0
>>  47 1  0  0  0
>>  48 1  0  0  0
>>  49 1  0  0  0
>>  50 1  0  0  0
>>
>> Quoting Mark Abraham <[EMAIL PROTECTED]>:
>>
>> > [EMAIL PROTECTED] wrote:
>> >
>> > Please generate replies to the mailing list sensibly. It's very hard to
>> > work out who you are quoting where in this email. It'd be easy just to
>> > ignore it, and that's the last thing you should want.
>> >
>> >> Hello,
>> >>
>> >> I'm trying to run a simulation with one lipid molecule in a fixed
>> >> simulation box without pbc.
>> >> I set position restraints on one of the atoms and I seem to keep on
>> >> getting the following error:
>> >
>> > Why do you want MD of a single lipid and a position restraint on one
>> > atom? If you just want to see a lipid wiggle around, then don't create
>> > more numerical complexity.
>> >
>> >> The lipid is DPPC.The .itp file I got from a coworker that used it
>> >> before for membrane MD simulations.
>> >> To minimize the system I used steepest descent with the following
>> >> parameters:
>> >
>> > Well if your grompp and mdrun completed successfully and without
>> > warnings then you've probably got an OK topology and structure.
>> >
>> > The combination of all bond constraints, a single lipid in vacuo,
>> > temperature coupling and a single position restraint sounds like a
>> > recipe for a numerical disaster, i.e. blowing up. Try with fewer of
>> > those things applied, or get a more physically-reasonable system, like
>> > a whole membrane.
>> >
>> > Mark
>> > ___
>> > gmx-users mailing listgmx-users@gromacs.org
>> > http://www.gromacs.org/mailman/listinfo/gmx-users
>> > Please search the archive at http://www.gromacs.org/search before
posting!
>> > Please don't post (un)subscribe re

Re: [gmx-users] position restraints

Quoting chandrabhan seniya <[EMAIL PROTECTED]>:

> what is yr real prob tell me?

No need to get confrontational; my reply was not intended to be insulting.  Mark
and I have been putting forth some effort to help our friend Gadi here by
extracting some detail that may be useful to document in the list archives. 
Posting advice to ignore the problem, that everything will be fine, etc, may
result in someone searching for help, finding your post about ignoring the
problem, and trying to proceed.  My response was simply that errors that cause
simulations to crash typically shouldn't be ignored with the belief that they
will resolve themselves.  Just my $0.02, and everyone hereafter is free to take
it or leave it.

-Justin

>
>
> On Thu, Apr 24, 2008 at 5:49 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
>
> > Quoting chandrabhan seniya <[EMAIL PROTECTED]>:
> >
> > > no prob you wait for some time it will write topology file and the
> > proceed
> > > further..
> >
> > I think that a lipid molecule trying to tear itself apart at step 0 would
> > fall
> > under the category of a "problem," and it will not disappear on it's own
> > if we
> > conveniently ignore it...
> >
> > >
> > > On Thu, Apr 24, 2008 at 5:04 PM, <[EMAIL PROTECTED]> wrote:
> > >
> > > > Hi,
> > > >
> > > > The full mdrun output when the simulation blows up is:
> > > >
> > > > Step 0, time 0 (ps)  LINCS WARNING
> > > > relative constraint deviation after LINCS:
> > > > max inf (between atoms 6 and 7) rms inf
> > > > bonds that rotated more than 30 degrees:
> > > > .
> > > > .
> > > > .
> > > > Warning: 1-4 interaction between 1 and 6 at distance
> > > > 324490777485109120.000 which is larger than the 1-4 table size 1.000
> > nm
> > > > These are ignored for the rest of the simulation
> > > > This usually means your system is exploding,
> > > > if not, you should increase table-extension in your mdp file
> > > >
> > > > Thanks Gadi
> > > >
> > > > Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>:
> > > >
> > > >
> > > > > Did your minimization converge to a nice, negative potential energy?
> > > > >  Also, what
> > > > > is the full mdrun output when the simulation blows up?  You've
> >  quoted
> > > > > the last
> > > > > bit, but it would be more informative to see the whole output, or at
> > > > > least a
> > > > > description of it (i.e., LINCS warnings).
> > > > >
> > > > > -Justin
> > > > >
> > > > > Quoting [EMAIL PROTECTED]:
> > > > >
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > I tried using no temperature coupling and no constraints, that did
> > not
> > > > > > help.
> > > > > > If I run the simulation without the position restraints it works
> > OK.
> > > > > > Could there by something wrong with the posre file (I'll attach it
> > at
> > > > > > the end of the email).
> > > > > > I want one of the atoms in the lipid to stay in one place and the
> > rest
> > > > > > to wiggle around it. Is there any other way to do that which is
> > not
> > > > > > position restraints.
> > > > > >
> > > > > > Thanks Gadi
> > > > > >
> > > > > >
> > > > > > [ position_restraints ]
> > > > > > ; atom  type  fx  fy  fz
> > > > > >  1 1  0  0  0
> > > > > >  2 1  0  0  0
> > > > > >  3 1  0  0  0
> > > > > >  4 1  0  0  0
> > > > > >  5 1  0  0  0
> > > > > >  6 1  0  0  0
> > > > > >  7 1  0  0  0
> > > > > >  8 1  1000.0  1000.0  1000.0
> > > > > >  9 1  0  0  0
> > > > > > 10 1  0  0  0
> > > > > > 11 1  0  0  0
> > > > > > 12 1  0  0  0
> > > > > > 13 1  0  0  0
> > > > > > 14 1  0  0  0
> > > > > > 15 1  0  0  0
> > > > > > 16 1  0  0  0
> > > > > > 17 1  0  0  0
> > > > > > 18 1  0  0  0
> > > > > > 19 1  0  0  0
> > > > > > 20 1  0  0  0
> > > > > > 21 1  0  0  0
> > > > > > 22 1  0  0  0
> > > > > > 23 1  0  0  0
> > > > > > 24 1  0  0  0
> > > > > > 25 1  0  0  0
> > > > > > 26 1  0  0  0
> > > > > > 27 1  0  0  0
> > > > > > 28 1  0  0  0
> > > > > > 29 1  0  0  0
> > > > > > 30 1  0  0  0
> > > > > > 31 1  0  0  0
> > > > > > 32 1  0  0  0
> > > > > > 33 1  0  0  0
> > > > > > 34 1  0  0  0
> > > > > > 35 1  0  0  0
> > > > > > 36 1  0  0  0
> > > > > > 37 1  0  0  0
> > > > > > 38 1  0  0  0
> > > > > > 39 1  0  0  0
> > > > > > 40 1  0  0  0
> > > > > > 41 1  0  0  0
> > > > > > 42 1  0  0  0
> > > > > > 43 1  0  0  0
> > > > > > 44 1  0  0  0
> > > > > > 45 1  0  0  0
> > > > > > 46 1  0  0  0
> > > > > > 47 1  0  0  0
> > > > > > 48 1  0  0  0
> > > > > > 49 1  0  0  0
> > > > > > 50 1  0  0  0
> > > > > >
> > > > > > Quoting Mark Abraham <[EMAIL PROTECTED]>:
> > > > > >
> > > > > > > [EMAIL PROTECTED] wrote:
>

Re: [gmx-users] position restraints

2008-04-24 Thread Mark Abraham


chandrabhan seniya wrote:

what is yr real prob tell me?


On this list, we like constructive criticism. I don't think the above 
qualifies as such.


Mark
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] position restraints

2008-04-24 Thread chandrabhan seniya

what is yr real prob tell me?


On Thu, Apr 24, 2008 at 5:49 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:

> Quoting chandrabhan seniya <[EMAIL PROTECTED]>:
>
> > no prob you wait for some time it will write topology file and the
> proceed
> > further..
>
> I think that a lipid molecule trying to tear itself apart at step 0 would
> fall
> under the category of a "problem," and it will not disappear on it's own
> if we
> conveniently ignore it...
>
> >
> > On Thu, Apr 24, 2008 at 5:04 PM, <[EMAIL PROTECTED]> wrote:
> >
> > > Hi,
> > >
> > > The full mdrun output when the simulation blows up is:
> > >
> > > Step 0, time 0 (ps)  LINCS WARNING
> > > relative constraint deviation after LINCS:
> > > max inf (between atoms 6 and 7) rms inf
> > > bonds that rotated more than 30 degrees:
> > > .
> > > .
> > > .
> > > Warning: 1-4 interaction between 1 and 6 at distance
> > > 324490777485109120.000 which is larger than the 1-4 table size 1.000
> nm
> > > These are ignored for the rest of the simulation
> > > This usually means your system is exploding,
> > > if not, you should increase table-extension in your mdp file
> > >
> > > Thanks Gadi
> > >
> > > Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>:
> > >
> > >
> > > > Did your minimization converge to a nice, negative potential energy?
> > > >  Also, what
> > > > is the full mdrun output when the simulation blows up?  You've
>  quoted
> > > > the last
> > > > bit, but it would be more informative to see the whole output, or at
> > > > least a
> > > > description of it (i.e., LINCS warnings).
> > > >
> > > > -Justin
> > > >
> > > > Quoting [EMAIL PROTECTED]:
> > > >
> > > >
> > > > > Hi,
> > > > >
> > > > > I tried using no temperature coupling and no constraints, that did
> not
> > > > > help.
> > > > > If I run the simulation without the position restraints it works
> OK.
> > > > > Could there by something wrong with the posre file (I'll attach it
> at
> > > > > the end of the email).
> > > > > I want one of the atoms in the lipid to stay in one place and the
> rest
> > > > > to wiggle around it. Is there any other way to do that which is
> not
> > > > > position restraints.
> > > > >
> > > > > Thanks Gadi
> > > > >
> > > > >
> > > > > [ position_restraints ]
> > > > > ; atom  type  fx  fy  fz
> > > > >  1 1  0  0  0
> > > > >  2 1  0  0  0
> > > > >  3 1  0  0  0
> > > > >  4 1  0  0  0
> > > > >  5 1  0  0  0
> > > > >  6 1  0  0  0
> > > > >  7 1  0  0  0
> > > > >  8 1  1000.0  1000.0  1000.0
> > > > >  9 1  0  0  0
> > > > > 10 1  0  0  0
> > > > > 11 1  0  0  0
> > > > > 12 1  0  0  0
> > > > > 13 1  0  0  0
> > > > > 14 1  0  0  0
> > > > > 15 1  0  0  0
> > > > > 16 1  0  0  0
> > > > > 17 1  0  0  0
> > > > > 18 1  0  0  0
> > > > > 19 1  0  0  0
> > > > > 20 1  0  0  0
> > > > > 21 1  0  0  0
> > > > > 22 1  0  0  0
> > > > > 23 1  0  0  0
> > > > > 24 1  0  0  0
> > > > > 25 1  0  0  0
> > > > > 26 1  0  0  0
> > > > > 27 1  0  0  0
> > > > > 28 1  0  0  0
> > > > > 29 1  0  0  0
> > > > > 30 1  0  0  0
> > > > > 31 1  0  0  0
> > > > > 32 1  0  0  0
> > > > > 33 1  0  0  0
> > > > > 34 1  0  0  0
> > > > > 35 1  0  0  0
> > > > > 36 1  0  0  0
> > > > > 37 1  0  0  0
> > > > > 38 1  0  0  0
> > > > > 39 1  0  0  0
> > > > > 40 1  0  0  0
> > > > > 41 1  0  0  0
> > > > > 42 1  0  0  0
> > > > > 43 1  0  0  0
> > > > > 44 1  0  0  0
> > > > > 45 1  0  0  0
> > > > > 46 1  0  0  0
> > > > > 47 1  0  0  0
> > > > > 48 1  0  0  0
> > > > > 49 1  0  0  0
> > > > > 50 1  0  0  0
> > > > >
> > > > > Quoting Mark Abraham <[EMAIL PROTECTED]>:
> > > > >
> > > > > > [EMAIL PROTECTED] wrote:
> > > > > >
> > > > > > Please generate replies to the mailing list sensibly. It's very
> hard
> > > > > to
> > > > > > work out who you are quoting where in this email. It'd be easy
> just
> > > > > to
> > > > > > ignore it, and that's the last thing you should want.
> > > > > >
> > > > > >> Hello,
> > > > > >>
> > > > > >> I'm trying to run a simulation with one lipid molecule in a
> fixed
> > > > > >> simulation box without pbc.
> > > > > >> I set position restraints on one of the atoms and I seem to
> keep on
> > > > > >> getting the following error:
> > > > > >
> > > > > > Why do you want MD of a single lipid and a position restraint on
> one
> > > > > > atom? If you just want to see a lipid wiggle around, then don't
> > > > > create
> > > > > > more numerical complexity.
> > > > > >
> > > > > >> The lipid is DPPC.The .itp file I got from a coworker that used
> it
> > > > > >> before for membrane MD simulations.
> > > > > >> To minimize the

Re: [gmx-users] position restraints

Quoting chandrabhan seniya <[EMAIL PROTECTED]>:

> no prob you wait for some time it will write topology file and the proceed
> further..

I think that a lipid molecule trying to tear itself apart at step 0 would fall
under the category of a "problem," and it will not disappear on it's own if we
conveniently ignore it...

>
> On Thu, Apr 24, 2008 at 5:04 PM, <[EMAIL PROTECTED]> wrote:
>
> > Hi,
> >
> > The full mdrun output when the simulation blows up is:
> >
> > Step 0, time 0 (ps)  LINCS WARNING
> > relative constraint deviation after LINCS:
> > max inf (between atoms 6 and 7) rms inf
> > bonds that rotated more than 30 degrees:
> > .
> > .
> > .
> > Warning: 1-4 interaction between 1 and 6 at distance
> > 324490777485109120.000 which is larger than the 1-4 table size 1.000 nm
> > These are ignored for the rest of the simulation
> > This usually means your system is exploding,
> > if not, you should increase table-extension in your mdp file
> >
> > Thanks Gadi
> >
> > Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>:
> >
> >
> > > Did your minimization converge to a nice, negative potential energy?
> > >  Also, what
> > > is the full mdrun output when the simulation blows up?  You've  quoted
> > > the last
> > > bit, but it would be more informative to see the whole output, or at
> > > least a
> > > description of it (i.e., LINCS warnings).
> > >
> > > -Justin
> > >
> > > Quoting [EMAIL PROTECTED]:
> > >
> > >
> > > > Hi,
> > > >
> > > > I tried using no temperature coupling and no constraints, that did not
> > > > help.
> > > > If I run the simulation without the position restraints it works OK.
> > > > Could there by something wrong with the posre file (I'll attach it at
> > > > the end of the email).
> > > > I want one of the atoms in the lipid to stay in one place and the rest
> > > > to wiggle around it. Is there any other way to do that which is not
> > > > position restraints.
> > > >
> > > > Thanks Gadi
> > > >
> > > >
> > > > [ position_restraints ]
> > > > ; atom  type  fx  fy  fz
> > > >  1 1  0  0  0
> > > >  2 1  0  0  0
> > > >  3 1  0  0  0
> > > >  4 1  0  0  0
> > > >  5 1  0  0  0
> > > >  6 1  0  0  0
> > > >  7 1  0  0  0
> > > >  8 1  1000.0  1000.0  1000.0
> > > >  9 1  0  0  0
> > > > 10 1  0  0  0
> > > > 11 1  0  0  0
> > > > 12 1  0  0  0
> > > > 13 1  0  0  0
> > > > 14 1  0  0  0
> > > > 15 1  0  0  0
> > > > 16 1  0  0  0
> > > > 17 1  0  0  0
> > > > 18 1  0  0  0
> > > > 19 1  0  0  0
> > > > 20 1  0  0  0
> > > > 21 1  0  0  0
> > > > 22 1  0  0  0
> > > > 23 1  0  0  0
> > > > 24 1  0  0  0
> > > > 25 1  0  0  0
> > > > 26 1  0  0  0
> > > > 27 1  0  0  0
> > > > 28 1  0  0  0
> > > > 29 1  0  0  0
> > > > 30 1  0  0  0
> > > > 31 1  0  0  0
> > > > 32 1  0  0  0
> > > > 33 1  0  0  0
> > > > 34 1  0  0  0
> > > > 35 1  0  0  0
> > > > 36 1  0  0  0
> > > > 37 1  0  0  0
> > > > 38 1  0  0  0
> > > > 39 1  0  0  0
> > > > 40 1  0  0  0
> > > > 41 1  0  0  0
> > > > 42 1  0  0  0
> > > > 43 1  0  0  0
> > > > 44 1  0  0  0
> > > > 45 1  0  0  0
> > > > 46 1  0  0  0
> > > > 47 1  0  0  0
> > > > 48 1  0  0  0
> > > > 49 1  0  0  0
> > > > 50 1  0  0  0
> > > >
> > > > Quoting Mark Abraham <[EMAIL PROTECTED]>:
> > > >
> > > > > [EMAIL PROTECTED] wrote:
> > > > >
> > > > > Please generate replies to the mailing list sensibly. It's very hard
> > > > to
> > > > > work out who you are quoting where in this email. It'd be easy just
> > > > to
> > > > > ignore it, and that's the last thing you should want.
> > > > >
> > > > >> Hello,
> > > > >>
> > > > >> I'm trying to run a simulation with one lipid molecule in a fixed
> > > > >> simulation box without pbc.
> > > > >> I set position restraints on one of the atoms and I seem to keep on
> > > > >> getting the following error:
> > > > >
> > > > > Why do you want MD of a single lipid and a position restraint on one
> > > > > atom? If you just want to see a lipid wiggle around, then don't
> > > > create
> > > > > more numerical complexity.
> > > > >
> > > > >> The lipid is DPPC.The .itp file I got from a coworker that used it
> > > > >> before for membrane MD simulations.
> > > > >> To minimize the system I used steepest descent with the following
> > > > >> parameters:
> > > > >
> > > > > Well if your grompp and mdrun completed successfully and without
> > > > > warnings then you've probably got an OK topology and structure.
> > > > >
> > > > > The combination of all bond constraints, a single lipid in vacuo,
> > > > > temperature coupling and a single position restraint sounds like a
> > > > > recipe for

Re: [gmx-users] position restraints

2008-04-24 Thread chandrabhan seniya

no prob you wait for some time it will write topology file and the proceed
further..

On Thu, Apr 24, 2008 at 5:04 PM, <[EMAIL PROTECTED]> wrote:

> Hi,
>
> The full mdrun output when the simulation blows up is:
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max inf (between atoms 6 and 7) rms inf
> bonds that rotated more than 30 degrees:
> .
> .
> .
> Warning: 1-4 interaction between 1 and 6 at distance
> 324490777485109120.000 which is larger than the 1-4 table size 1.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
>
> Thanks Gadi
>
> Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>:
>
>
> > Did your minimization converge to a nice, negative potential energy?
> >  Also, what
> > is the full mdrun output when the simulation blows up?  You've  quoted
> > the last
> > bit, but it would be more informative to see the whole output, or at
> > least a
> > description of it (i.e., LINCS warnings).
> >
> > -Justin
> >
> > Quoting [EMAIL PROTECTED]:
> >
> >
> > > Hi,
> > >
> > > I tried using no temperature coupling and no constraints, that did not
> > > help.
> > > If I run the simulation without the position restraints it works OK.
> > > Could there by something wrong with the posre file (I'll attach it at
> > > the end of the email).
> > > I want one of the atoms in the lipid to stay in one place and the rest
> > > to wiggle around it. Is there any other way to do that which is not
> > > position restraints.
> > >
> > > Thanks Gadi
> > >
> > >
> > > [ position_restraints ]
> > > ; atom  type  fx  fy  fz
> > >  1 1  0  0  0
> > >  2 1  0  0  0
> > >  3 1  0  0  0
> > >  4 1  0  0  0
> > >  5 1  0  0  0
> > >  6 1  0  0  0
> > >  7 1  0  0  0
> > >  8 1  1000.0  1000.0  1000.0
> > >  9 1  0  0  0
> > > 10 1  0  0  0
> > > 11 1  0  0  0
> > > 12 1  0  0  0
> > > 13 1  0  0  0
> > > 14 1  0  0  0
> > > 15 1  0  0  0
> > > 16 1  0  0  0
> > > 17 1  0  0  0
> > > 18 1  0  0  0
> > > 19 1  0  0  0
> > > 20 1  0  0  0
> > > 21 1  0  0  0
> > > 22 1  0  0  0
> > > 23 1  0  0  0
> > > 24 1  0  0  0
> > > 25 1  0  0  0
> > > 26 1  0  0  0
> > > 27 1  0  0  0
> > > 28 1  0  0  0
> > > 29 1  0  0  0
> > > 30 1  0  0  0
> > > 31 1  0  0  0
> > > 32 1  0  0  0
> > > 33 1  0  0  0
> > > 34 1  0  0  0
> > > 35 1  0  0  0
> > > 36 1  0  0  0
> > > 37 1  0  0  0
> > > 38 1  0  0  0
> > > 39 1  0  0  0
> > > 40 1  0  0  0
> > > 41 1  0  0  0
> > > 42 1  0  0  0
> > > 43 1  0  0  0
> > > 44 1  0  0  0
> > > 45 1  0  0  0
> > > 46 1  0  0  0
> > > 47 1  0  0  0
> > > 48 1  0  0  0
> > > 49 1  0  0  0
> > > 50 1  0  0  0
> > >
> > > Quoting Mark Abraham <[EMAIL PROTECTED]>:
> > >
> > > > [EMAIL PROTECTED] wrote:
> > > >
> > > > Please generate replies to the mailing list sensibly. It's very hard
> > > to
> > > > work out who you are quoting where in this email. It'd be easy just
> > > to
> > > > ignore it, and that's the last thing you should want.
> > > >
> > > >> Hello,
> > > >>
> > > >> I'm trying to run a simulation with one lipid molecule in a fixed
> > > >> simulation box without pbc.
> > > >> I set position restraints on one of the atoms and I seem to keep on
> > > >> getting the following error:
> > > >
> > > > Why do you want MD of a single lipid and a position restraint on one
> > > > atom? If you just want to see a lipid wiggle around, then don't
> > > create
> > > > more numerical complexity.
> > > >
> > > >> The lipid is DPPC.The .itp file I got from a coworker that used it
> > > >> before for membrane MD simulations.
> > > >> To minimize the system I used steepest descent with the following
> > > >> parameters:
> > > >
> > > > Well if your grompp and mdrun completed successfully and without
> > > > warnings then you've probably got an OK topology and structure.
> > > >
> > > > The combination of all bond constraints, a single lipid in vacuo,
> > > > temperature coupling and a single position restraint sounds like a
> > > > recipe for a numerical disaster, i.e. blowing up. Try with fewer of
> > > > those things applied, or get a more physically-reasonable system,
> > > like
> > > > a whole membrane.
> > > >
> > > > Mark
> > > > ___
> > > > gmx-users mailing listgmx-users@gromacs.org
> > > > http://www.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

Re: [gmx-users] position restraints

Quoting [EMAIL PROTECTED]:

> Hi,
>
> The full mdrun output when the simulation blows up is:
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max inf (between atoms 6 and 7) rms inf
> bonds that rotated more than 30 degrees:
>   .
>   .
>   .
> Warning: 1-4 interaction between 1 and 6 at distance
> 324490777485109120.000 which is larger than the 1-4 table size 1.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file

Basic information about this type of error can be found here (as well as several
hundred posts in the list archive):

http://wiki.gromacs.org/index.php/Errors#LINCS_warnings

How did you do your minimization, with or without restraints?  Did it converge
to an acceptable potential energy?

-Justin

>
> Thanks Gadi
>
> Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>:
>
> >
> > Did your minimization converge to a nice, negative potential energy?
> >   Also, what
> > is the full mdrun output when the simulation blows up?  You've
> > quoted the last
> > bit, but it would be more informative to see the whole output, or at least
> a
> > description of it (i.e., LINCS warnings).
> >
> > -Justin
> >
> > Quoting [EMAIL PROTECTED]:
> >
> >>
> >> Hi,
> >>
> >> I tried using no temperature coupling and no constraints, that did not
> help.
> >> If I run the simulation without the position restraints it works OK.
> >> Could there by something wrong with the posre file (I'll attach it at
> >> the end of the email).
> >> I want one of the atoms in the lipid to stay in one place and the rest
> >> to wiggle around it. Is there any other way to do that which is not
> >> position restraints.
> >>
> >> Thanks Gadi
> >>
> >>
> >> [ position_restraints ]
> >> ; atom  type  fx  fy  fz
> >>   1 1  0  0  0
> >>   2 1  0  0  0
> >>   3 1  0  0  0
> >>   4 1  0  0  0
> >>   5 1  0  0  0
> >>   6 1  0  0  0
> >>   7 1  0  0  0
> >>   8 1  1000.0  1000.0  1000.0
> >>   9 1  0  0  0
> >>  10 1  0  0  0
> >>  11 1  0  0  0
> >>  12 1  0  0  0
> >>  13 1  0  0  0
> >>  14 1  0  0  0
> >>  15 1  0  0  0
> >>  16 1  0  0  0
> >>  17 1  0  0  0
> >>  18 1  0  0  0
> >>  19 1  0  0  0
> >>  20 1  0  0  0
> >>  21 1  0  0  0
> >>  22 1  0  0  0
> >>  23 1  0  0  0
> >>  24 1  0  0  0
> >>  25 1  0  0  0
> >>  26 1  0  0  0
> >>  27 1  0  0  0
> >>  28 1  0  0  0
> >>  29 1  0  0  0
> >>  30 1  0  0  0
> >>  31 1  0  0  0
> >>  32 1  0  0  0
> >>  33 1  0  0  0
> >>  34 1  0  0  0
> >>  35 1  0  0  0
> >>  36 1  0  0  0
> >>  37 1  0  0  0
> >>  38 1  0  0  0
> >>  39 1  0  0  0
> >>  40 1  0  0  0
> >>  41 1  0  0  0
> >>  42 1  0  0  0
> >>  43 1  0  0  0
> >>  44 1  0  0  0
> >>  45 1  0  0  0
> >>  46 1  0  0  0
> >>  47 1  0  0  0
> >>  48 1  0  0  0
> >>  49 1  0  0  0
> >>  50 1  0  0  0
> >>
> >> Quoting Mark Abraham <[EMAIL PROTECTED]>:
> >>
> >> > [EMAIL PROTECTED] wrote:
> >> >
> >> > Please generate replies to the mailing list sensibly. It's very hard to
> >> > work out who you are quoting where in this email. It'd be easy just to
> >> > ignore it, and that's the last thing you should want.
> >> >
> >> >> Hello,
> >> >>
> >> >> I'm trying to run a simulation with one lipid molecule in a fixed
> >> >> simulation box without pbc.
> >> >> I set position restraints on one of the atoms and I seem to keep on
> >> >> getting the following error:
> >> >
> >> > Why do you want MD of a single lipid and a position restraint on one
> >> > atom? If you just want to see a lipid wiggle around, then don't create
> >> > more numerical complexity.
> >> >
> >> >> The lipid is DPPC.The .itp file I got from a coworker that used it
> >> >> before for membrane MD simulations.
> >> >> To minimize the system I used steepest descent with the following
> >> >> parameters:
> >> >
> >> > Well if your grompp and mdrun completed successfully and without
> >> > warnings then you've probably got an OK topology and structure.
> >> >
> >> > The combination of all bond constraints, a single lipid in vacuo,
> >> > temperature coupling and a single position restraint sounds like a
> >> > recipe for a numerical disaster, i.e. blowing up. Try with fewer of
> >> > those things applied, or get a more physically-reasonable system, like
> >> > a whole membrane.
> >> >
> >> > Mark
> >> > ___
> >> > gmx-users mailing listgmx-users@gromacs.org
> >> > http://www.gromacs.org/mailman/listinfo/gmx-users
> >> > Please search the archive at http://www.

Re: [gmx-users] position restraints

Hi,

The full mdrun output when the simulation blows up is:

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max inf (between atoms 6 and 7) rms inf
bonds that rotated more than 30 degrees:
 .
 .
 .
Warning: 1-4 interaction between 1 and 6 at distance  
324490777485109120.000 which is larger than the 1-4 table size 1.000 nm

These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file

Thanks Gadi

Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>:

Did your minimization converge to a nice, negative potential energy?  
  Also, what
is the full mdrun output when the simulation blows up?  You've   
quoted the last

bit, but it would be more informative to see the whole output, or at least a
description of it (i.e., LINCS warnings).

-Justin

Quoting [EMAIL PROTECTED]:

Hi,

I tried using no temperature coupling and no constraints, that did not help.
If I run the simulation without the position restraints it works OK.
Could there by something wrong with the posre file (I'll attach it at
the end of the email).
I want one of the atoms in the lipid to stay in one place and the rest
to wiggle around it. Is there any other way to do that which is not
position restraints.

Thanks Gadi

[ position_restraints ]
; atom  type  fx  fy  fz
  1 1  0  0  0
  2 1  0  0  0
  3 1  0  0  0
  4 1  0  0  0
  5 1  0  0  0
  6 1  0  0  0
  7 1  0  0  0
  8 1  1000.0  1000.0  1000.0
  9 1  0  0  0
 10 1  0  0  0
 11 1  0  0  0
 12 1  0  0  0
 13 1  0  0  0
 14 1  0  0  0
 15 1  0  0  0
 16 1  0  0  0
 17 1  0  0  0
 18 1  0  0  0
 19 1  0  0  0
 20 1  0  0  0
 21 1  0  0  0
 22 1  0  0  0
 23 1  0  0  0
 24 1  0  0  0
 25 1  0  0  0
 26 1  0  0  0
 27 1  0  0  0
 28 1  0  0  0
 29 1  0  0  0
 30 1  0  0  0
 31 1  0  0  0
 32 1  0  0  0
 33 1  0  0  0
 34 1  0  0  0
 35 1  0  0  0
 36 1  0  0  0
 37 1  0  0  0
 38 1  0  0  0
 39 1  0  0  0
 40 1  0  0  0
 41 1  0  0  0
 42 1  0  0  0
 43 1  0  0  0
 44 1  0  0  0
 45 1  0  0  0
 46 1  0  0  0
 47 1  0  0  0
 48 1  0  0  0
 49 1  0  0  0
 50 1  0  0  0

Quoting Mark Abraham <[EMAIL PROTECTED]>:

> [EMAIL PROTECTED] wrote:
>
> Please generate replies to the mailing list sensibly. It's very hard to
> work out who you are quoting where in this email. It'd be easy just to
> ignore it, and that's the last thing you should want.
>
>> Hello,
>>
>> I'm trying to run a simulation with one lipid molecule in a fixed
>> simulation box without pbc.
>> I set position restraints on one of the atoms and I seem to keep on
>> getting the following error:
>
> Why do you want MD of a single lipid and a position restraint on one
> atom? If you just want to see a lipid wiggle around, then don't create
> more numerical complexity.
>
>> The lipid is DPPC.The .itp file I got from a coworker that used it
>> before for membrane MD simulations.
>> To minimize the system I used steepest descent with the following
>> parameters:
>
> Well if your grompp and mdrun completed successfully and without
> warnings then you've probably got an OK topology and structure.
>
> The combination of all bond constraints, a single lipid in vacuo,
> temperature coupling and a single position restraint sounds like a
> recipe for a numerical disaster, i.e. blowing up. Try with fewer of
> those things applied, or get a more physically-reasonable system, like
> a whole membrane.
>
> Mark
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.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 [EMAIL PROTECTED]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

This message was sent using IMP, the Internet Messaging Program.

___
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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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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080

Re: [gmx-users] position restraints

2008-04-24 Thread Mark Abraham


[EMAIL PROTECTED] wrote:


Hi,

I tried using no temperature coupling and no constraints, that did not 
help.

If I run the simulation without the position restraints it works OK.


OK, so they're (interacting with something else to be) generating a 
numerical problem.


Could there by something wrong with the posre file (I'll attach it at 
the end of the email).
I want one of the atoms in the lipid to stay in one place and the rest 
to wiggle around it. Is there any other way to do that which is not 
position restraints.


After the fact, you could choose to translate any atom of your choice to 
a fixed point and the system with it, using (say) VMD. It wouldn't mean 
much of anything, apart from probably no longer being a simulation in an 
inertial reference frame.


Unless there's a meaningful purpose to seeing such a thing in a test 
run, it's really not worth anyone's time. If there is, then explaining 
it the first time makes you sound much more like someone with a real 
issue, than someone just trying to make something fit some preconception 
about pleasant appearance.



Thanks Gadi


[ position_restraints ]
; atom  type  fx  fy  fz
 1 1  0  0  0
 2 1  0  0  0
 3 1  0  0  0
 4 1  0  0  0
 5 1  0  0  0
 6 1  0  0  0
 7 1  0  0  0
 8 1  1000.0  1000.0  1000.0
 9 1  0  0  0
10 1  0  0  0
11 1  0  0  0
12 1  0  0  0
13 1  0  0  0
14 1  0  0  0
15 1  0  0  0
16 1  0  0  0
17 1  0  0  0
18 1  0  0  0
19 1  0  0  0
20 1  0  0  0
21 1  0  0  0
22 1  0  0  0
23 1  0  0  0
24 1  0  0  0
25 1  0  0  0
26 1  0  0  0
27 1  0  0  0
28 1  0  0  0
29 1  0  0  0
30 1  0  0  0
31 1  0  0  0
32 1  0  0  0
33 1  0  0  0
34 1  0  0  0
35 1  0  0  0
36 1  0  0  0
37 1  0  0  0
38 1  0  0  0
39 1  0  0  0
40 1  0  0  0
41 1  0  0  0
42 1  0  0  0
43 1  0  0  0
44 1  0  0  0
45 1  0  0  0
46 1  0  0  0
47 1  0  0  0
48 1  0  0  0
49 1  0  0  0
50 1  0  0  0


That's probably fine if grompp doesn't complain - but you can delete all 
the position restraints with zero force, since they are doing nothing.


Mark
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Re: [gmx-users] position restraints


Did your minimization converge to a nice, negative potential energy?  Also, what
is the full mdrun output when the simulation blows up?  You've quoted the last
bit, but it would be more informative to see the whole output, or at least a
description of it (i.e., LINCS warnings).

-Justin

Quoting [EMAIL PROTECTED]:

>
> Hi,
>
> I tried using no temperature coupling and no constraints, that did not help.
> If I run the simulation without the position restraints it works OK.
> Could there by something wrong with the posre file (I'll attach it at
> the end of the email).
> I want one of the atoms in the lipid to stay in one place and the rest
> to wiggle around it. Is there any other way to do that which is not
> position restraints.
>
> Thanks Gadi
>
>
> [ position_restraints ]
> ; atom  type  fx  fy  fz
>   1 1  0  0  0
>   2 1  0  0  0
>   3 1  0  0  0
>   4 1  0  0  0
>   5 1  0  0  0
>   6 1  0  0  0
>   7 1  0  0  0
>   8 1  1000.0  1000.0  1000.0
>   9 1  0  0  0
>  10 1  0  0  0
>  11 1  0  0  0
>  12 1  0  0  0
>  13 1  0  0  0
>  14 1  0  0  0
>  15 1  0  0  0
>  16 1  0  0  0
>  17 1  0  0  0
>  18 1  0  0  0
>  19 1  0  0  0
>  20 1  0  0  0
>  21 1  0  0  0
>  22 1  0  0  0
>  23 1  0  0  0
>  24 1  0  0  0
>  25 1  0  0  0
>  26 1  0  0  0
>  27 1  0  0  0
>  28 1  0  0  0
>  29 1  0  0  0
>  30 1  0  0  0
>  31 1  0  0  0
>  32 1  0  0  0
>  33 1  0  0  0
>  34 1  0  0  0
>  35 1  0  0  0
>  36 1  0  0  0
>  37 1  0  0  0
>  38 1  0  0  0
>  39 1  0  0  0
>  40 1  0  0  0
>  41 1  0  0  0
>  42 1  0  0  0
>  43 1  0  0  0
>  44 1  0  0  0
>  45 1  0  0  0
>  46 1  0  0  0
>  47 1  0  0  0
>  48 1  0  0  0
>  49 1  0  0  0
>  50 1  0  0  0
>
> Quoting Mark Abraham <[EMAIL PROTECTED]>:
>
> > [EMAIL PROTECTED] wrote:
> >
> > Please generate replies to the mailing list sensibly. It's very hard to
> > work out who you are quoting where in this email. It'd be easy just to
> > ignore it, and that's the last thing you should want.
> >
> >> Hello,
> >>
> >> I'm trying to run a simulation with one lipid molecule in a fixed
> >> simulation box without pbc.
> >> I set position restraints on one of the atoms and I seem to keep on
> >> getting the following error:
> >
> > Why do you want MD of a single lipid and a position restraint on one
> > atom? If you just want to see a lipid wiggle around, then don't create
> > more numerical complexity.
> >
> >> The lipid is DPPC.The .itp file I got from a coworker that used it
> >> before for membrane MD simulations.
> >> To minimize the system I used steepest descent with the following
> >> parameters:
> >
> > Well if your grompp and mdrun completed successfully and without
> > warnings then you've probably got an OK topology and structure.
> >
> > The combination of all bond constraints, a single lipid in vacuo,
> > temperature coupling and a single position restraint sounds like a
> > recipe for a numerical disaster, i.e. blowing up. Try with fewer of
> > those things applied, or get a more physically-reasonable system, like
> > a whole membrane.
> >
> > Mark
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
> > http://www.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 [EMAIL PROTECTED]
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
> 
> This message was sent using IMP, the Internet Messaging Program.
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.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 [EMAIL PROTECTED]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>





Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/


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Please don't post (un)subscribe requests to the list. Us

Re: [gmx-users] position restraints



Hi,

I tried using no temperature coupling and no constraints, that did not help.
If I run the simulation without the position restraints it works OK.
Could there by something wrong with the posre file (I'll attach it at  
the end of the email).
I want one of the atoms in the lipid to stay in one place and the rest  
to wiggle around it. Is there any other way to do that which is not  
position restraints.


Thanks Gadi


[ position_restraints ]
; atom  type  fx  fy  fz
 1 1  0  0  0
 2 1  0  0  0
 3 1  0  0  0
 4 1  0  0  0
 5 1  0  0  0
 6 1  0  0  0
 7 1  0  0  0
 8 1  1000.0  1000.0  1000.0
 9 1  0  0  0
10 1  0  0  0
11 1  0  0  0
12 1  0  0  0
13 1  0  0  0
14 1  0  0  0
15 1  0  0  0
16 1  0  0  0
17 1  0  0  0
18 1  0  0  0
19 1  0  0  0
20 1  0  0  0
21 1  0  0  0
22 1  0  0  0
23 1  0  0  0
24 1  0  0  0
25 1  0  0  0
26 1  0  0  0
27 1  0  0  0
28 1  0  0  0
29 1  0  0  0
30 1  0  0  0
31 1  0  0  0
32 1  0  0  0
33 1  0  0  0
34 1  0  0  0
35 1  0  0  0
36 1  0  0  0
37 1  0  0  0
38 1  0  0  0
39 1  0  0  0
40 1  0  0  0
41 1  0  0  0
42 1  0  0  0
43 1  0  0  0
44 1  0  0  0
45 1  0  0  0
46 1  0  0  0
47 1  0  0  0
48 1  0  0  0
49 1  0  0  0
50 1  0  0  0

Quoting Mark Abraham <[EMAIL PROTECTED]>:


[EMAIL PROTECTED] wrote:

Please generate replies to the mailing list sensibly. It's very hard to
work out who you are quoting where in this email. It'd be easy just to
ignore it, and that's the last thing you should want.


Hello,

I'm trying to run a simulation with one lipid molecule in a fixed
simulation box without pbc.
I set position restraints on one of the atoms and I seem to keep on
getting the following error:


Why do you want MD of a single lipid and a position restraint on one
atom? If you just want to see a lipid wiggle around, then don't create
more numerical complexity.

The lipid is DPPC.The .itp file I got from a coworker that used it   
before for membrane MD simulations.
To minimize the system I used steepest descent with the following   
parameters:


Well if your grompp and mdrun completed successfully and without
warnings then you've probably got an OK topology and structure.

The combination of all bond constraints, a single lipid in vacuo,
temperature coupling and a single position restraint sounds like a
recipe for a numerical disaster, i.e. blowing up. Try with fewer of
those things applied, or get a more physically-reasonable system, like
a whole membrane.

Mark
___
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Re: [gmx-users] position restraints

2008-04-24 Thread Mark Abraham


[EMAIL PROTECTED] wrote:

Please generate replies to the mailing list sensibly. It's very hard to 
work out who you are quoting where in this email. It'd be easy just to 
ignore it, and that's the last thing you should want.



Hello,

I'm trying to run a simulation with one lipid molecule in a fixed
simulation box without pbc.
I set position restraints on one of the atoms and I seem to keep on
getting the following error:


Why do you want MD of a single lipid and a position restraint on one 
atom? If you just want to see a lipid wiggle around, then don't create 
more numerical complexity.


The lipid is DPPC.The .itp file I got from a coworker that used it 
before for membrane MD simulations.
To minimize the system I used steepest descent with the following 
parameters:


Well if your grompp and mdrun completed successfully and without 
warnings then you've probably got an OK topology and structure.


The combination of all bond constraints, a single lipid in vacuo, 
temperature coupling and a single position restraint sounds like a 
recipe for a numerical disaster, i.e. blowing up. Try with fewer of 
those things applied, or get a more physically-reasonable system, like a 
whole membrane.


Mark
___
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Re: [gmx-users] position restraints