[gmx-users] how to prepare implicit solvent system??

2011-04-19 Thread 김현식 

Dear experts,

hi, I'm using Gromacs for implicit solvent system, Can anybody let me know hot 
to prepare the implicit solvent system??

Thanks
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Re: [gmx-users] how to prepare implicit solvent system??

2011-04-19 Thread Justin A. Lemkul 



김현식 wrote:

Dear experts,

hi, I'm using Gromacs for implicit solvent system, Can anybody let me 
know hot to prepare the implicit solvent system??




Just as you would any other system, except you don't need to define a unit cell 
full of water and ions.  pdb2gmx, grompp, mdrun.  There are benchmarks and 
example input files on the Gromacs site.


-Justin


Thanks



--


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] how to prepare implicit solvent system??

2011-04-19 Thread Justin A. Lemkul 



김현식 wrote:

If i want to use implicit solvent, genbox step is indispensable ?
or Just GBSA in mdp file can effect like solvation ?



It sounds like you need to do a bit of literature/textbook reading before you 
continue.  If you're using implicit solvent, then you don't need explicit 
solvent.  That's sort of the point.


-Justin


  Date: Tue, 19 Apr 2011 09:49:25 -0400
  From: jalem...@vt.edu
  To: gmx-users@gromacs.org
  Subject: Re: [gmx-users] how to prepare implicit solvent system??
 
 
 
  김현식 wrote:
   Dear experts,
  
   hi, I'm using Gromacs for implicit solvent system, Can anybody let me
   know hot to prepare the implicit solvent system??
  
 
  Just as you would any other system, except you don't need to define a 
unit cell

  full of water and ions. pdb2gmx, grompp, mdrun. There are benchmarks and
  example input files on the Gromacs site.
 
  -Justin
 
   Thanks
  
 
  --
  
 
  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/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.
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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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