Re: [gmx-users] Position Restrained Simulation for Coarse Grained DSPC

2010-06-23 Thread Justin A. Lemkul



sunny mishra wrote:

Hi,

Thanks a lot for the quick reply. I want to position restrain the head 
group atoms of CG DSPC  but I am not sure about the head group molecules 
in DSPC. Can you please tell me how to figure out the head group atoms 


Presumably there is a structure of DSPC somewhere you can refer to.  I would 
think you should know the chemical features of the structures they are 
simulating before diving right in blindly :)


or molecules. Also, when you say co-ordinate file then you mean .itp 
file for the lipid right?


No, I mean coordinate file.  An .itp is a topology.

-Justin



Thanks

On Wed, Jun 23, 2010 at 2:47 PM, Justin A. Lemkul > wrote:




sunny mishra wrote:

Dear All,

I am trying to run the Position Restrained simulation for the
Coarse Grained DSPC bi-layer. However, I am quite confused that
how to generate the position restraint file for the CG atoms in
lipid. Is there a difference between the position restraint file
for the fine grained and coarse grained structures. Please let
me know how to generate the position restraint file for Coarse
Grained DSPC bi-layer. Your reply for the same will be highly
appreciable.


You can generate a position restraint file for any molecule using
genrestr. Just make sure to supply it with a coordinate file for a
single molecule (i.e., not your entire bilayer), since position
restraints are applied to moleculetypes, and not global structures.

-Justin


Thanks,

Sunny


-- 



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 Restrained Simulation for Coarse Grained DSPC

2010-06-23 Thread sunny mishra
Hi,

Thanks a lot for the quick reply. I want to position restrain the head group
atoms of CG DSPC  but I am not sure about the head group molecules in DSPC.
Can you please tell me how to figure out the head group atoms or molecules.
Also, when you say co-ordinate file then you mean .itp file for the lipid
right?

Thanks

On Wed, Jun 23, 2010 at 2:47 PM, Justin A. Lemkul  wrote:

>
>
> sunny mishra wrote:
>
>> Dear All,
>>
>> I am trying to run the Position Restrained simulation for the Coarse
>> Grained DSPC bi-layer. However, I am quite confused that how to generate the
>> position restraint file for the CG atoms in lipid. Is there a difference
>> between the position restraint file for the fine grained and coarse grained
>> structures. Please let me know how to generate the position restraint file
>> for Coarse Grained DSPC bi-layer. Your reply for the same will be highly
>> appreciable.
>>
>
> You can generate a position restraint file for any molecule using genrestr.
> Just make sure to supply it with a coordinate file for a single molecule
> (i.e., not your entire bilayer), since position restraints are applied to
> moleculetypes, and not global structures.
>
> -Justin
>
>
>> Thanks,
>>
>> Sunny
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
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Re: [gmx-users] Position Restrained Simulation for Coarse Grained DSPC

2010-06-23 Thread Justin A. Lemkul



sunny mishra wrote:

Dear All,

I am trying to run the Position Restrained simulation for the Coarse 
Grained DSPC bi-layer. However, I am quite confused that how to generate 
the position restraint file for the CG atoms in lipid. Is there a 
difference between the position restraint file for the fine grained and 
coarse grained structures. Please let me know how to generate the 
position restraint file for Coarse Grained DSPC bi-layer. Your reply for 
the same will be highly appreciable.


You can generate a position restraint file for any molecule using genrestr. 
Just make sure to supply it with a coordinate file for a single molecule (i.e., 
not your entire bilayer), since position restraints are applied to 
moleculetypes, and not global structures.


-Justin



Thanks,

Sunny



--


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] Position Restrained Simulation for Coarse Grained DSPC

2010-06-23 Thread sunny mishra
Dear All,

I am trying to run the Position Restrained simulation for the Coarse Grained
DSPC bi-layer. However, I am quite confused that how to generate the
position restraint file for the CG atoms in lipid. Is there a difference
between the position restraint file for the fine grained and coarse grained
structures. Please let me know how to generate the position restraint file
for Coarse Grained DSPC bi-layer. Your reply for the same will be highly
appreciable.

Thanks,

Sunny
-- 
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