[gmx-users] Something about getting started

[Justin A. Lemkul]

DreamCatcher wrote:
> Dear gmx-users,
>       I am a freshman of gmx and I wanna use gromacs for 
> polyvinyl-alcohol simulation.But I don't even know how to start it.

Then start simple with some tutorial material:

http://oldwiki.gromacs.org/index.php/Tutorials

>       Is it necessary to start my simulation with a .pdb files?If 

You need some sort of structure to start with; .pdb files are generally the 
starting point.

> so,What should I do before this?I can make an pdb file for a chain of 
> syndiotatic polyvinyl-alcohols via Material Studio or some other 
> packages,but the residue cann't be recognize,so I have to modify some 
> top files to correct it.I just modify the .hdb and rtp files endeavor to 
> make it.But it seems not an easy work.

Indeed, it is not.  I again suggest you start with some basic tutorials with 
robust systems so you learn the workflow of a Gromacs simulation.  Once you've 
got a handle on how everything flows, then attempt your system.

For polymers, you may find this thread useful:

http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html

-Justin

>      the message the package sent to me is as follows,appreciate if 
> somebody can help me to handle this!
> *** (this is an previous version.when i try to use pdb2gmx to get its 
> .top file,a fatal error reminds:
>      "source code file : resall.c line:279 ()
>        Fatal errors:
>             in .rtp file at line :    "
>      when I add the charge and chargegroupndx of the atoms,there comes a 
> similar error  ):
> My attempt is as follows:
> ###  in rtp file
> [ VAB ]
>  [ atoms ]
>   CB  opls_135
>   HB1  opls_140
>   HB2  opls_140
>   HB3  opls_140
>    CA  opls_158
>   HA1  opls_140
>    OH  opls_154
>    HO  opls_155
>   
>  [ bonds ]
>    CB  HB1
>    CB  HB2
>    CB  HB3
>    CB   CA
>    CA  HA1
>    CA   OH
>    OH   HO
>    CA  +CB
>   
> [VA ]
>  [ atoms ]
>     CB  opls_136
>    HB1  opls_140
>    HB2  opls_140
>     CA  opls_158 
>    HA1  opls_140
>    OA  opls_154
>   HOA  opls_155
>    CG  opls_136
>   HG1  opls_140
>   HG2  opls_140
>    CD  opls_158
>    HD  opls_140
>    OD  opls_154
>   HOD  opls_155
>     
>  [ bonds ]
>    CB    -CA
>    CB   HB1
>    CB   HB2
>    CB    CA
>    CA   HA1
>    CA   OH
>    OH   HO
>    CA    CG
>    CG   HG1
>    CG   HG2
>    CG   CD
>    CD    HD
>    CD   OD
>    OD   HOD
>    CD   +CB
>   
> [VAE]
>  [ atoms ]
>    CB  opls_136
>    HB1  opls_140
>    HB2  opls_140
>     CA  opls_157
>    HA1  opls_140
>    HA2  opls_140
>    OH  opls_154
>    HO  opls_155
>    
>  [ bonds ]
>    CB  -CD
>    CB  HB1
>    CB  HB2
>    CB   CA
>    CA  HA1
>    CA  HA2
>    CA   OH
>    OH   HO
>  
> #### in .hdb file:
> ; H add type H i j k
> VAB    3
> 3 4 HB  CB  CA  +CB
> 1 5 HA  CA  CB  +CB
> 1 2 HO  OH  CA  +CB
> VA      6
> 2 6 HB  CB  CA  -CA
> 1 5 HA  CA  CB   CG
> 1 2 HOA OA  CA   CG
> 2 6 HG  CG  CA   CD
> 1 5 HD  CD  CG  +CB
> 1 1 HOD OD  CD  CG
> VAE     3
> 2 6 HB  CB  CA  -CD
> 2 6 HA  CA  CB  +CB
> 1 2 HO  OH  CA  +CB
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
========================================

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

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