Re: [gmx-users] Simulation of a protein confined in a box

[Omer Markovitch]

In short - you can apply PBC in all directions (XYZ) by choosing the proper
keyword in the .mdp file, I believe the box dimensions are defined in .gro
file.
Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Fri, Oct 10, 2008 at 16:00, Lee Soin <[EMAIL PROTECTED]> wrote:

> Maybe I didn't put it clearly. My intention is to simulate a protein
> confined in a box, and the problem is that I don't know how to define a
> boundary, or a wall, in GROMACS.
>
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[gmx-users] How to confine a protein in a box?

[Lee Soin]

Hello, all! I intend to simulate a protein confined in a box. Can anybody
tell me how to define a boundary, or a wall, in GROMACS? Thanks!

-- 
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Department of Physics
Nanjing University, China
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Re: [gmx-users] simulation of mixed enantiomers

[Alan Dodd]

The topologies should not be identical, surely?  Check out the section on 
improper dihedrals in the manual, it's possible to specify an improper to keep 
enantiomers in their intended handedness. 



- Original Message 
From: Anthony Costa <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Friday, October 10, 2008 8:45:55 PM
Subject: [gmx-users] simulation of mixed enantiomers

i have a simulation where i would like to study the interaction of N
small molecules of various enantiomeric composition.

if i use a simple R+S situation (N=2) by inserting the other
enantiomer into my already created box, subsequent minimization either
yields unphysical structures for the inserted enantiomer or will often
reverse its symmetry to that of the original molecule. i am clearly
missing something about the configuration of a reasonable topology for
this type of system, but i'm can't quite figure it out.

not surprisingly, i get errors when creating the mdp file for my
energy minimization. the topologies created for both R and S
enantiomers are identical, as i would expect (in this case they are
small amino acid residues), when created individually, so i usually
just increment the number of molecules in my original topology file
after inserting the opposite enantiomer.

WARNING 1 [file "topol.top", line 159]:
13 non-matching atom names
atom names from topol.top will be used
atom names from 2_2mer.gro will be ignored

what am i missing?

thanks for your time,
anthony

--
Anthony B. Costa
Purdue University
Department of Chemistry
560 Oval Drive, #365
West Lafayette, IN 47907
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Re: [gmx-users] simulation of mixed enantiomers

[Justin A. Lemkul]

Anthony Costa wrote:

i have a simulation where i would like to study the interaction of N
small molecules of various enantiomeric composition.

if i use a simple R+S situation (N=2) by inserting the other
enantiomer into my already created box, subsequent minimization either
yields unphysical structures for the inserted enantiomer or will often
reverse its symmetry to that of the original molecule. i am clearly
missing something about the configuration of a reasonable topology for
this type of system, but i'm can't quite figure it out.

not surprisingly, i get errors when creating the mdp file for my
energy minimization. the topologies created for both R and S
enantiomers are identical, as i would expect (in this case they are
small amino acid residues), when created individually, so i usually
just increment the number of molecules in my original topology file
after inserting the opposite enantiomer.



Probably the parameters you are applying the enantiomers are either uniform, or 
inconsistent.  In other words, some R molecules are taking S parameters, and 
some are taking R parameters, and the same for the S molecules.


The easiest way to deal with this (as I have done in the case of mixed bilayers) 
is to place everything in the same order, in both the .top and the .gro.  For 
example, say you have two topologies - r.itp and s.itp - that you apply to the R 
and S molecules, respectively.  In the .top, you would:


#include "r.itp"
#include "s.itp"

In the [molecules] section, you would have to have:

R   x
S   x

...where 'x' is the number of each molecule type.  If different parameters are 
being applied, they cannot be grouped, which I think is what you are doing.


In the .gro file, all the R molecules would then have to appear before the S 
molecules.  If this is not the case with your .gro, it can easily be fixed using 
standard Unix tools like grep and cat.



WARNING 1 [file "topol.top", line 159]:
 13 non-matching atom names
 atom names from topol.top will be used
 atom names from 2_2mer.gro will be ignored


Also probably from the inconsistencies I described above.



what am i missing?

thanks for your time,
anthony

--
Anthony B. Costa
Purdue University
Department of Chemistry
560 Oval Drive, #365
West Lafayette, IN 47907
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--


Justin A. Lemkul
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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[gmx-users] simulation of mixed enantiomers

[Anthony Costa]

i have a simulation where i would like to study the interaction of N
small molecules of various enantiomeric composition.

if i use a simple R+S situation (N=2) by inserting the other
enantiomer into my already created box, subsequent minimization either
yields unphysical structures for the inserted enantiomer or will often
reverse its symmetry to that of the original molecule. i am clearly
missing something about the configuration of a reasonable topology for
this type of system, but i'm can't quite figure it out.

not surprisingly, i get errors when creating the mdp file for my
energy minimization. the topologies created for both R and S
enantiomers are identical, as i would expect (in this case they are
small amino acid residues), when created individually, so i usually
just increment the number of molecules in my original topology file
after inserting the opposite enantiomer.

WARNING 1 [file "topol.top", line 159]:
 13 non-matching atom names
 atom names from topol.top will be used
 atom names from 2_2mer.gro will be ignored

what am i missing?

thanks for your time,
anthony

--
Anthony B. Costa
Purdue University
Department of Chemistry
560 Oval Drive, #365
West Lafayette, IN 47907
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[gmx-users] Opinion: Can position restraining waters increase the speed of the md simulation?

[Arthur Roberts]

Hi, all,


In a previous email, I asked about the availability of implicit water  
calculations in Gromacs 4.0, which might be available in Gromacs 4.1.   
In the meantime, I was wondering if I position restrained waters that  
are 6 Angstroms from the protein, would that increase the speed of md  
simulation, if I have a water shell that extends 15 Angstroms.  I  
would appreciate your input.


Best wishes,
Art Roberts
University of Washington


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Re: [gmx-users] Running MD only for selected part of molecule

[Samuel Coulbourn Flores 花山]

You might want to try Simbody (simtk.org).  This will allow you to  
rigidify any part or parts of the molecule you choose.  As a bonus,  
you will not spend resources computing intramolecular interactions in  
the rigidified regions.


Sam

On Oct 10, 2008, at 6:10 AM, Justin A. Lemkul wrote:




vivek sharma wrote:

Hi justin,
My apologies for asking you so many small queries.
Can you suggest any good tutorial or reference that talks about  
this issue of running MD over a selected part of molecule.


If you're using PR, all you're doing is position-restrained dynamics.

-Justin


With Thanks,
Vivek
2008/10/10 vivek sharma <[EMAIL PROTECTED] >

   hI justin,
   Thanks for your response.
   do I need to specify the index file(for residue that I want to  
keep

   fix during MD) during GROMPP or just including the psre.itp in
   topology is enough for the purpose ?
   With Thanks,
   Vivek
   2008/10/10 Justin A. Lemkul <[EMAIL PROTECTED] >

   Justin A. Lemkul wrote:
   vivek sharma wrote:
   Thanks Justin,
   My goal is to keep certain part fixed and move only a
   few of the residues (case is like providing  
flexibility

   to the site of interest only).
   SO , do I need to specify the residue using some index
   file ?
   or is  there some other way to specify the part of
   molecule for position restraining ??
   Make an index file with the residues you want to keep fixed,  
and

   pass it
   to genpr to generate a new posre.itp that corresponds to those
   residues.
   -Justin
   With Thanks,
   Vivek
   2008/10/10 Justin A. Lemkul <[EMAIL PROTECTED]
    >>
  vivek sharma wrote:
  Hi there,
   I want to run MD over a part of my molecule ,
   for few residues
  only (not the whole molecule).
  Can I do it using GROMACS ?
  I searched for the online documentation and
   mailing list, but
  unable to get appropriate information.
  If somebody has already tried such things
   earlier, please
  suggest and direct me for appropriate link and
   address.
  Well, if your goal is to keep certain parts fixed  
and

   allow others
  to move, probably the easiest way to do it is to
   apply position
  restraints to the "fixed" part.
  -Justin
  With Thanks,
  Vivek
  


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  Graduate Research Assistant
  Department of Biochemistry
  Virginia Tech
  Blacksburg, VA
  jalemkul[at]vt.edu  vt.edu> |

   (540) 231-9080
  http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
  
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[gmx-users] .tdb entries for polystyrene (or other linear polymer)

[Andrea Muntean]

Sorry for the trivial question, but I am new in Gromacs. I try to simulate a
polystyrene film and I want to use a 8.pdb file from an equilibrated film of
32 chains, 80 monomers each. I unterstand that I should enter the residues
(for the first, inner and last monomer(s)) and maybe to define the correct
parameters in the *.itp file(s). But it is still not clear to me how to
define the conectivity between the monomers.
Can somebody help me? I saw there are some people simulating polymers with
gromacs. Please help!

Thank you for any help,

Andrea
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Re: [gmx-users] Simulation of a protein confined in a box

[Lee Soin]

Maybe I didn't put it clearly. My intention is to simulate a protein
confined in a box, and the problem is that I don't know how to define a
boundary, or a wall, in GROMACS.

2008/10/10 Omer Markovitch <[EMAIL PROTECTED]>

> Boundary should not "precisely" be around the protein, otherwise some parts
> of the protein would "feel" other parts via the boundary.
> In general, if you apply periodic boundary conditions (PBC), take the
> dimensions as such so the protein would NOT feel the PBC.
>
> Say you have an unfolded protein (or a MD during which a protein unfolds)
> whose length is about 20 Angstroms, and you use no explicit solvent. You
> might not want to take the dimension of the box to be smaller they, say, 40
> Angstroms.
> Its just an example.
>
> Omer.
>
> Koby Levy research group,
> Weizmann Institute of Science.
> http://www.weizmann.ac.il/sb/faculty_pages/Levy/
>
>
> On Fri, Oct 10, 2008 at 11:03, Lee Soin <[EMAIL PROTECTED]> wrote:
>
>> But the problem is: how to define a boundary?
>>
>
>
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-- 
Sun Li
Department of Physics
Nanjing University, China
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Re: [gmx-users] Converting 2-d molecule to 3-D

[Florian Haberl]

Hi,

On Friday, 10. October 2008, andrea spitaleri wrote:
> Hi there,
> have look to "corina" software. I dont think it is free.
> http://cheminf.cmbi.ru.nl/cheminf/corina/

corina is a commerical product see

http://www.molecular-networks.com/software/corina/

You can try cdk it should convert 2d to 3d or any other chem(o)informatic 
toolkit.

Also something like MOE can handle such task.

Greetings,

Florian

>
> and
>
> vivek sharma wrote:
> > Hi there,
> >
> > Is there any open source package to convert 2-D structure of a molecule
> > to 3-D structure ?
> > If anybody have tried such thing, please suggest  me te way to do the
> > same. I am having openbabel  on my system, does openbabel i shaving such
> > functionality ?
> >
> > please suggest ?
> >
> >
> > With thanks,
> > Vivek
> >
> >
> >
> > 
> >
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-- 
---
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 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone: +49(0) − 9131 − 85 26573
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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Re: [gmx-users] Running MD only for selected part of molecule

[Justin A. Lemkul]

vivek sharma wrote:

Hi justin,

My apologies for asking you so many small queries.
Can you suggest any good tutorial or reference that talks about this 
issue of running MD over a selected part of molecule.


If you're using PR, all you're doing is position-restrained dynamics.

-Justin



With Thanks,
Vivek

2008/10/10 vivek sharma <[EMAIL PROTECTED] 
>


hI justin,

Thanks for your response.
do I need to specify the index file(for residue that I want to keep
fix during MD) during GROMPP or just including the psre.itp in
topology is enough for the purpose ?


With Thanks,
Vivek

2008/10/10 Justin A. Lemkul <[EMAIL PROTECTED] >



Justin A. Lemkul wrote:



vivek sharma wrote:

Thanks Justin,

My goal is to keep certain part fixed and move only a
few of the residues (case is like providing flexibility
to the site of interest only).
SO , do I need to specify the residue using some index
file ?
or is  there some other way to specify the part of
molecule for position restraining ??


Make an index file with the residues you want to keep fixed, and
pass it
to genpr to generate a new posre.itp that corresponds to those
residues.

-Justin


With Thanks,
Vivek


2008/10/10 Justin A. Lemkul <[EMAIL PROTECTED]
 >>



   vivek sharma wrote:

   Hi there,
I want to run MD over a part of my molecule ,
for few residues
   only (not the whole molecule).
   Can I do it using GROMACS ?
   I searched for the online documentation and
mailing list, but
   unable to get appropriate information.
   If somebody has already tried such things
earlier, please
   suggest and direct me for appropriate link and
address.


   Well, if your goal is to keep certain parts fixed and
allow others
   to move, probably the easiest way to do it is to
apply position
   restraints to the "fixed" part.

   -Justin

   With Thanks,
   Vivek


 
 


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   Justin A. Lemkul
   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] Running MD only for selected part of molecule

[Justin A. Lemkul]

vivek sharma wrote:

hI justin,

Thanks for your response.
do I need to specify the index file(for residue that I want to keep fix 
during MD) during GROMPP or just including the psre.itp in topology is 
enough for the purpose ?


No; you just need it to pass to genpr.

Please remember to copy the list on your questions and responses!

-Justin



With Thanks,
Vivek

2008/10/10 Justin A. Lemkul <[EMAIL PROTECTED] >



Justin A. Lemkul wrote:



vivek sharma wrote:

Thanks Justin,

My goal is to keep certain part fixed and move only a few of
the residues (case is like providing flexibility to the site
of interest only).
SO , do I need to specify the residue using some index file ?
or is  there some other way to specify the part of molecule
for position restraining ??


Make an index file with the residues you want to keep fixed, and pass it
to genpr to generate a new posre.itp that corresponds to those residues.

-Justin


With Thanks,
Vivek


2008/10/10 Justin A. Lemkul <[EMAIL PROTECTED]
 >>



   vivek sharma wrote:

   Hi there,
I want to run MD over a part of my molecule , for
few residues
   only (not the whole molecule).
   Can I do it using GROMACS ?
   I searched for the online documentation and mailing
list, but
   unable to get appropriate information.
   If somebody has already tried such things earlier, please
   suggest and direct me for appropriate link and address.


   Well, if your goal is to keep certain parts fixed and
allow others
   to move, probably the easiest way to do it is to apply
position
   restraints to the "fixed" part.

   -Justin

   With Thanks,
   Vivek


 
 


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   -- 

   Justin A. Lemkul
   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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-- 



Justin A. Lemkul
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] Converting 2-d molecule to 3-D

[Justin A. Lemkul]

Use the PRODRG server; it is free:

http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta

-Justin

andrea spitaleri wrote:

Hi there,
have look to "corina" software. I dont think it is free.
http://cheminf.cmbi.ru.nl/cheminf/corina/

and

vivek sharma wrote:

Hi there,

Is there any open source package to convert 2-D structure of a 
molecule to

3-D structure ?
If anybody have tried such thing, please suggest  me te way to do the 
same.

I am having openbabel  on my system, does openbabel i shaving such
functionality ?

please suggest ?


With thanks,
Vivek





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--


Justin A. Lemkul
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] Running MD only for selected part of molecule

[vivek sharma]

Hi justin,

My apologies for asking you so many small queries.
Can you suggest any good tutorial or reference that talks about this issue
of running MD over a selected part of molecule.

With Thanks,
Vivek

2008/10/10 vivek sharma <[EMAIL PROTECTED]>

> hI justin,
>
> Thanks for your response.
> do I need to specify the index file(for residue that I want to keep fix
> during MD) during GROMPP or just including the psre.itp in topology is
> enough for the purpose ?
>
>
> With Thanks,
> Vivek
>
> 2008/10/10 Justin A. Lemkul <[EMAIL PROTECTED]>
>
>>
>>
>> Justin A. Lemkul wrote:
>>
>>>
>>>
>>> vivek sharma wrote:
>>>
 Thanks Justin,

 My goal is to keep certain part fixed and move only a few of the
 residues (case is like providing flexibility to the site of interest only).
 SO , do I need to specify the residue using some index file ?
 or is  there some other way to specify the part of molecule for position
 restraining ??


>> Make an index file with the residues you want to keep fixed, and pass it
>> to genpr to generate a new posre.itp that corresponds to those residues.
>>
>> -Justin
>>
>>
 With Thanks,
 Vivek


 2008/10/10 Justin A. Lemkul <[EMAIL PROTECTED] >



vivek sharma wrote:

Hi there,
 I want to run MD over a part of my molecule , for few residues
only (not the whole molecule).
Can I do it using GROMACS ?
I searched for the online documentation and mailing list, but
unable to get appropriate information.
If somebody has already tried such things earlier, please
suggest and direct me for appropriate link and address.


Well, if your goal is to keep certain parts fixed and allow others
to move, probably the easiest way to do it is to apply position
restraints to the "fixed" part.

-Justin

With Thanks,
Vivek



  

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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
>> 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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>
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Re: [gmx-users] Converting 2-d molecule to 3-D

[andrea spitaleri]

Hi there,
have look to "corina" software. I dont think it is free.
http://cheminf.cmbi.ru.nl/cheminf/corina/

and

vivek sharma wrote:

Hi there,

Is there any open source package to convert 2-D structure of a molecule to
3-D structure ?
If anybody have tried such thing, please suggest  me te way to do the same.
I am having openbabel  on my system, does openbabel i shaving such
functionality ?

please suggest ?


With thanks,
Vivek





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--
---
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
Tel: 0039-0226434348/5622/3497/4922
Fax: 0039-0226434153
---
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Re: [gmx-users] Running MD only for selected part of molecule

[vivek sharma]

hI justin,

Thanks for your response.
do I need to specify the index file(for residue that I want to keep fix
during MD) during GROMPP or just including the psre.itp in topology is
enough for the purpose ?

With Thanks,
Vivek

2008/10/10 Justin A. Lemkul <[EMAIL PROTECTED]>

>
>
> Justin A. Lemkul wrote:
>
>>
>>
>> vivek sharma wrote:
>>
>>> Thanks Justin,
>>>
>>> My goal is to keep certain part fixed and move only a few of the residues
>>> (case is like providing flexibility to the site of interest only).
>>> SO , do I need to specify the residue using some index file ?
>>> or is  there some other way to specify the part of molecule for position
>>> restraining ??
>>>
>>>
> Make an index file with the residues you want to keep fixed, and pass it
> to genpr to generate a new posre.itp that corresponds to those residues.
>
> -Justin
>
>
>>> With Thanks,
>>> Vivek
>>>
>>>
>>> 2008/10/10 Justin A. Lemkul <[EMAIL PROTECTED] >
>>>
>>>
>>>
>>>vivek sharma wrote:
>>>
>>>Hi there,
>>> I want to run MD over a part of my molecule , for few residues
>>>only (not the whole molecule).
>>>Can I do it using GROMACS ?
>>>I searched for the online documentation and mailing list, but
>>>unable to get appropriate information.
>>>If somebody has already tried such things earlier, please
>>>suggest and direct me for appropriate link and address.
>>>
>>>
>>>Well, if your goal is to keep certain parts fixed and allow others
>>>to move, probably the easiest way to do it is to apply position
>>>restraints to the "fixed" part.
>>>
>>>-Justin
>>>
>>>With Thanks,
>>>Vivek
>>>
>>>
>>>
>>>  
>>>
>>>___
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>>>
>>>http://www.gromacs.org/mailman/listinfo/gmx-users
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>>>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
>>>jalemkul[at]vt.edu  | (540) 231-9080
>>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>>
>>>___
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>>>.
>>>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
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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[gmx-users] Converting 2-d molecule to 3-D

[vivek sharma]

Hi there,

Is there any open source package to convert 2-D structure of a molecule to
3-D structure ?
If anybody have tried such thing, please suggest  me te way to do the same.
I am having openbabel  on my system, does openbabel i shaving such
functionality ?

please suggest ?


With thanks,
Vivek
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Re: [gmx-users] Running MD only for selected part of molecule

[Justin A. Lemkul]

Justin A. Lemkul wrote:



vivek sharma wrote:

Thanks Justin,

My goal is to keep certain part fixed and move only a few of the 
residues (case is like providing flexibility to the site of interest 
only).

SO , do I need to specify the residue using some index file ?
or is  there some other way to specify the part of molecule for 
position restraining ??




Make an index file with the residues you want to keep fixed, and pass it
to genpr to generate a new posre.itp that corresponds to those residues.

-Justin



With Thanks,
Vivek


2008/10/10 Justin A. Lemkul <[EMAIL PROTECTED] >



vivek sharma wrote:

Hi there,
 I want to run MD over a part of my molecule , for few residues
only (not the whole molecule).
Can I do it using GROMACS ?
I searched for the online documentation and mailing list, but
unable to get appropriate information.
If somebody has already tried such things earlier, please
suggest and direct me for appropriate link and address.


Well, if your goal is to keep certain parts fixed and allow others
to move, probably the easiest way to do it is to apply position
restraints to the "fixed" part.

-Justin

With Thanks,
Vivek






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-- 

Justin A. Lemkul
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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--


Justin A. Lemkul
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] Running MD only for selected part of molecule

[vivek sharma]

Thanks Justin,

My goal is to keep certain part fixed and move only a few of the residues
(case is like providing flexibility to the site of interest only).
SO , do I need to specify the residue using some index file ?
or is  there some other way to specify the part of molecule for position
restraining ??


With Thanks,
Vivek


2008/10/10 Justin A. Lemkul <[EMAIL PROTECTED]>

>
>
> vivek sharma wrote:
>
>> Hi there,
>>  I want to run MD over a part of my molecule , for few residues only (not
>> the whole molecule).
>> Can I do it using GROMACS ?
>> I searched for the online documentation and mailing list, but unable to
>> get appropriate information.
>> If somebody has already tried such things earlier, please suggest and
>> direct me for appropriate link and address.
>>
>>
> Well, if your goal is to keep certain parts fixed and allow others to move,
> probably the easiest way to do it is to apply position restraints to the
> "fixed" part.
>
> -Justin
>
>  With Thanks,
>> Vivek
>>
>>
>> 
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
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>
> --
> 
>
> Justin A. Lemkul
> 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] Running MD only for selected part of molecule

[Justin A. Lemkul]

vivek sharma wrote:

Hi there,
 
I want to run MD over a part of my molecule , for few residues only (not 
the whole molecule).

Can I do it using GROMACS ?
I searched for the online documentation and mailing list, but unable to 
get appropriate information.
If somebody has already tried such things earlier, please suggest and 
direct me for appropriate link and address.




Well, if your goal is to keep certain parts fixed and allow others to move, 
probably the easiest way to do it is to apply position restraints to the "fixed" 
part.


-Justin


With Thanks,
Vivek




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--


Justin A. Lemkul
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] Continuing a crashed run when running simulation in parts

[Justin A. Lemkul]

vivek sharma wrote:

Hi There,
I am running a long MDS for one protein molecule in water, To avoid 
error I am running the simulation in parts like 20 nsec each.

Each time I am creating a new tpr, trr and edr using the tpbconv and mdrun.
Last time when I fired a job for 60-80 nsec then the job crashed because 
of some power supply problem. Now I want to continue the job from where 
it crashed ..

while using . tpbconv with tpr, trr and edr file it gave me message like
_---
trn version: GMX_trn_file (double precision)
Read frame  4: step  0 time 6.000

Using frame of step 0 time 6
Opened emprmd_np24.edr as double precision energy file
Reading frame  0 time 6.000  


READ 3 PRESSURE COUPLING MU'S FROM emprmd_np24.edr

4000 steps (8 ps) remaining from first run.
Writing statusfile with starting step  0 and length   4000 
steps...

 time  0.000 and length  8.000 ps
-

above message indicates that it is going to start the run from step 0, 
which seems waste for me
Can I continue the job from where it crashed, or is it better to run the 
60-80 nsec job again?




Depending on the frequency with which you write to the .trr and .edr (nstxout, 
nstvout, nstenergy) there may be nothing in those files except the initial 
frame.  Use gmxcheck to confirm this.


-Justin



With Thanks,
Vivek




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--


Justin A. Lemkul
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] Installation on iMAC

[Justin A. Lemkul]

Kwee Hong wrote:

Hi.

I'm very new to iMAC as I've just started to use it for about one month. 
I would like to install GROMACS on it but i seem can't find any 
step-to-step installation instruction. All those that I found was seem 
to be instruction for linux. Can you give me some idea on how to get the 
installation instruction?




The installation is the same if you are compiling from source.

-Justin


Thank you very much.


Best regards,

Joyssstan




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--


Justin A. Lemkul
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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[gmx-users] Re: QMMM - Gaussian source compilation (Eudes Fileti)

[ggroenh]

I have created a wiki entry on this:

http://wiki.gromacs.org/index.php/compiling_QMMM


Gerrit


--
Gerrit Groenhof
MPI biophysical chemistry
Goettingen
Germany
http://www.mpibpc.mpg.de/groups/grubmueller/start/people/ggroenh/index.html

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[gmx-users] Running MD only for selected part of molecule

[vivek sharma]

Hi there,

I want to run MD over a part of my molecule , for few residues only (not the
whole molecule).
Can I do it using GROMACS ?
I searched for the online documentation and mailing list, but unable to get
appropriate information.
If somebody has already tried such things earlier, please suggest and direct
me for appropriate link and address.

With Thanks,
Vivek
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Re: [gmx-users] Simulation of a protein confined in a box

[Omer Markovitch]

Boundary should not "precisely" be around the protein, otherwise some parts
of the protein would "feel" other parts via the boundary.
In general, if you apply periodic boundary conditions (PBC), take the
dimensions as such so the protein would NOT feel the PBC.

Say you have an unfolded protein (or a MD during which a protein unfolds)
whose length is about 20 Angstroms, and you use no explicit solvent. You
might not want to take the dimension of the box to be smaller they, say, 40
Angstroms.
Its just an example.

Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Fri, Oct 10, 2008 at 11:03, Lee Soin <[EMAIL PROTECTED]> wrote:

> But the problem is: how to define a boundary?
>
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Re: [gmx-users] Simulation of a protein confined in a box

[Lee Soin]

But the problem is: how to define a boundary?

2008/10/10 Xavier Periole <[EMAIL PROTECTED]>

> On Fri, 10 Oct 2008 15:09:31 +0800
>  "Lee Soin" <[EMAIL PROTECTED]> wrote:
>
>> Hi! I'm going to simulate a protein confined in a box. Can GROMACS do
>> this?
>> Will the removal of the periodic boundary condition be OK?
>>
> The removal of the periodic boundary conditions will be equivalent to an
> infinite box. Unless you define the boundaries of your box (e.g. walls)
> the protein (in solvent?) would not stop diffusing. This no problem but
> is this what you like?
>
>>
>> --
>> Sun Li
>> Department of Physics
>> Nanjing University, China
>>
>
> -
> XAvier Periole - PhD
>
> - Molecular Dynamics Group -
> NMR and Computation
> University of Groningen
> The Netherlands
> -
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-- 
Sun Li
Department of Physics
Nanjing University, China
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Re: [gmx-users] Simulation of a protein confined in a box

[Xavier Periole]

On Fri, 10 Oct 2008 15:09:31 +0800
 "Lee Soin" <[EMAIL PROTECTED]> wrote:

Hi! I'm going to simulate a protein confined in a box. Can GROMACS do this?
Will the removal of the periodic boundary condition be OK?

The removal of the periodic boundary conditions will be equivalent to an
infinite box. Unless you define the boundaries of your box (e.g. walls)
the protein (in solvent?) would not stop diffusing. This no problem but
is this what you like?


--
Sun Li
Department of Physics
Nanjing University, China


-
XAvier Periole - PhD

- Molecular Dynamics Group -
NMR and Computation
University of Groningen
The Netherlands
-
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[gmx-users] Simulation of a protein confined in a box

[Lee Soin]

Hi! I'm going to simulate a protein confined in a box. Can GROMACS do this?
Will the removal of the periodic boundary condition be OK?

-- 
Sun Li
Department of Physics
Nanjing University, China
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