Re: [gmx-users] Polymer simulation help and suggestions

[Justin A. Lemkul]

Caleb Tormey wrote:

Justin,
Thank you for your response.  My simulation will involve around 30 
chains of polymer along with varying amounts of different salts.  For 
instance LiPF6, LiClO4 and larger molecules like 
[1,3-dimethylimidazolium]PF6 and I am looking for the best way to 
incorporate these.  I guess I am a little stumped as to the best method 
for generating these.  Should I make separate .gro and topology files 
for these? 


Yes.  You won't be able to add these polyatomic ions with genion.  You will have 
to insert them with genbox -ci -nmol instead, then #include the relevant .itp 
files into your .top file.


Parameterization of these compounds will not be trivial.  You should be prepared 
for significant effort to develop these parameters for the force field you've 
chosen, unless they've already been developed and validated.


http://www.gromacs.org/Documentation/How-tos/Parameterization

-Justin


Regards,
Caleb
PS.  I haven't researched this part as much so it is possible this has 
already been answered and I just haven't come across this. 



On Sun, May 23, 2010 at 10:47 AM, Justin A. Lemkul > wrote:




Caleb Tormey wrote:

Hello all,
I have just started working with GROMACS and simulation in
general.  I will be doing simulation of PEO with various ions
and need a little help.  I have read a great deal of the
documentation and now edited the appropriate .rtp and.itp files
to generate my polymer from a .pdb file using pdb2gmx and it
seems to be generating my topology and .gro files correctly.
My question is if I wish to keep a static bond length do I
address this in the bond information or is there something in
the .mdp file that will address this?


Use the "constraints" keyword in your .mdp file.  See the manual.


I also would like some suggestions for a few other things.  To
make my preliminary polymer I used a molecular modeling/editor
program called Avogadro but was wondering if there is something
better to use to create the random walk long chain polymer?


There are several programs that can build molecules, like xLeap
(part of AmberTools) and even VMD has some capabilities for building
molecules.  I don't know about polymers specifically.


Also, I was just going to create my own ion files and use genion
to incorporate those into the simulation but didn't know if this
was the best way to do this.


To what files are you referring?  Are you introducing new parameters
of some sort?  Be aware that pre-defined ion parameters are included
as part of all the force field parameter sets packaged with Gromacs,
so any new parameters must be validated before being used.


And lastly when I need to create a multiple polymer simulation
my plan was to use genconf and generate a crystal with the
appropriate number of polymers and then just heat it up to melt
it.  This seems to be a good way to do it however, another
person in my group who used NAMD used a program called PackMol
and had some success and was wondering if anyone else had used
this program and would recommend this route?


Either way should work fine.  PackMol does a good job of generating
initial configurations given geometrical constraints, but your
procedure should work if you do sufficient heating to change the
initial structure.

-Justin


Thank you in advanced.
Regards,
Caleb


-- 



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] Polymer simulation help and suggestions

[Caleb Tormey]

Justin,
Thank you for your response.  My simulation will involve around 30 chains of
polymer along with varying amounts of different salts.  For instance LiPF6,
LiClO4 and larger molecules like [1,3-dimethylimidazolium]PF6 and I am
looking for the best way to incorporate these.  I guess I am a little
stumped as to the best method for generating these.  Should I make separate
.gro and topology files for these?
Regards,
Caleb
PS.  I haven't researched this part as much so it is possible this has
already been answered and I just haven't come across this.


On Sun, May 23, 2010 at 10:47 AM, Justin A. Lemkul  wrote:

>
>
> Caleb Tormey wrote:
>
>> Hello all,
>> I have just started working with GROMACS and simulation in general.  I
>> will be doing simulation of PEO with various ions and need a little help.  I
>> have read a great deal of the documentation and now edited the appropriate
>> .rtp and.itp files to generate my polymer from a .pdb file using pdb2gmx and
>> it seems to be generating my topology and .gro files correctly.
>> My question is if I wish to keep a static bond length do I address this in
>> the bond information or is there something in the .mdp file that will
>> address this?
>>
>
> Use the "constraints" keyword in your .mdp file.  See the manual.
>
>
>  I also would like some suggestions for a few other things.  To make my
>> preliminary polymer I used a molecular modeling/editor program called
>> Avogadro but was wondering if there is something better to use to create the
>> random walk long chain polymer?
>>
>
> There are several programs that can build molecules, like xLeap (part of
> AmberTools) and even VMD has some capabilities for building molecules.  I
> don't know about polymers specifically.
>
>
>  Also, I was just going to create my own ion files and use genion to
>> incorporate those into the simulation but didn't know if this was the best
>> way to do this.
>>
>>
> To what files are you referring?  Are you introducing new parameters of
> some sort?  Be aware that pre-defined ion parameters are included as part of
> all the force field parameter sets packaged with Gromacs, so any new
> parameters must be validated before being used.
>
>
>  And lastly when I need to create a multiple polymer simulation my plan was
>> to use genconf and generate a crystal with the appropriate number of
>> polymers and then just heat it up to melt it.  This seems to be a good way
>> to do it however, another person in my group who used NAMD used a program
>> called PackMol and had some success and was wondering if anyone else had
>> used this program and would recommend this route?
>>
>>
> Either way should work fine.  PackMol does a good job of generating initial
> configurations given geometrical constraints, but your procedure should work
> if you do sufficient heating to change the initial structure.
>
> -Justin
>
>
>  Thank you in advanced.
>> Regards,
>> Caleb
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
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>
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Re: [gmx-users] Polymer simulation help and suggestions

[Justin A. Lemkul]

Caleb Tormey wrote:

Hello all,
I have just started working with GROMACS and simulation in general.  I 
will be doing simulation of PEO with various ions and need a little 
help.  I have read a great deal of the documentation and now edited the 
appropriate .rtp and.itp files to generate my polymer from a .pdb file 
using pdb2gmx and it seems to be generating my topology and .gro files 
correctly. 

My question is if I wish to keep a static bond length do I address this 
in the bond information or is there something in the .mdp file that will 
address this? 



Use the "constraints" keyword in your .mdp file.  See the manual.

I also would like some suggestions for a few other things.  To make my 
preliminary polymer I used a molecular modeling/editor program called 
Avogadro but was wondering if there is something better to use to create 
the random walk long chain polymer? 



There are several programs that can build molecules, like xLeap (part of 
AmberTools) and even VMD has some capabilities for building molecules.  I don't 
know about polymers specifically.


Also, I was just going to create my own ion files and use genion to 
incorporate those into the simulation but didn't know if this was the 
best way to do this.




To what files are you referring?  Are you introducing new parameters of some 
sort?  Be aware that pre-defined ion parameters are included as part of all the 
force field parameter sets packaged with Gromacs, so any new parameters must be 
validated before being used.


And lastly when I need to create a multiple polymer simulation my plan 
was to use genconf and generate a crystal with the appropriate number of 
polymers and then just heat it up to melt it.  This seems to be a good 
way to do it however, another person in my group who used NAMD used a 
program called PackMol and had some success and was wondering if anyone 
else had used this program and would recommend this route?




Either way should work fine.  PackMol does a good job of generating initial 
configurations given geometrical constraints, but your procedure should work if 
you do sufficient heating to change the initial structure.


-Justin


Thank you in advanced.
Regards,
Caleb



--


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


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[gmx-users] Polymer simulation help and suggestions

[Caleb Tormey]

Hello all,
I have just started working with GROMACS and simulation in general.  I will
be doing simulation of PEO with various ions and need a little help.  I have
read a great deal of the documentation and now edited the appropriate .rtp
and.itp files to generate my polymer from a .pdb file using pdb2gmx and it
seems to be generating my topology and .gro files correctly.

My question is if I wish to keep a static bond length do I address this in
the bond information or is there something in the .mdp file that will
address this?

I also would like some suggestions for a few other things.  To make my
preliminary polymer I used a molecular modeling/editor program called
Avogadro but was wondering if there is something better to use to create the
random walk long chain polymer?

Also, I was just going to create my own ion files and use genion to
incorporate those into the simulation but didn't know if this was the best
way to do this.

And lastly when I need to create a multiple polymer simulation my plan was
to use genconf and generate a crystal with the appropriate number of
polymers and then just heat it up to melt it.  This seems to be a good way
to do it however, another person in my group who used NAMD used a program
called PackMol and had some success and was wondering if anyone else had
used this program and would recommend this route?

Thank you in advanced.
Regards,
Caleb
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RE: [gmx-users] polymer simulation

[Dallas B. Warren]

If you are referring to something that will generate a coordinate file
(.pdb or .gro) of polymer molecules randomly distributed, then there is
not currently a script with GROMACS that will do that job.  If you have
a single molecule, there are a couple of tools that can randomly spread
those molecules around, though not very well.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.
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[gmx-users] polymer simulation

[Sudip Roy]

Dear all,

I would like to know that is there any gromacs tool which can generate a
polymer melt?
If not, is there any tool you can suggest which can do the job.

Thank you.

Sudip

--
**

Dr. Sudip Roy
Physical Chemistry and Material Science Division
Scientist C
National Chemical Laboratory
Pune 411008
India

Tel.  +91 2590 2735 Office
Email s@ncl.res.in



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