jojo J wrote:
Hello Mark,
Thank you for your reply. AS for the steps you mentioned to solvate a
molecule: I have a simple molecule replicated by genconf -nbox in one
direction. When I try to energy minimize this single molecule grompp em
gives error: rlist is longer than half box size or longer than shortest
diagnal boz size... I increase the size and everything is fine but can
you please tell me what is the criterion to specify the size. Does
boxsize affect results in MD? ( I am asking this because if I want to
use genconf to replicate this molecule which is in a large boxzise the
final size of the system can become very large so I have to use
editconf to reduce the size again)
http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention
...and perhaps some textbook reading. If you make a system too small, you'll
waste a whole lot of time generating meaningless trajectories.
Also sometimes some parts of the molcule in the box are outside the box
when I see the trajectory (ngmx) at the beginning.. and I think because
of the pbc it jups inthebox from the otherside. Should the particle be
entirely in box at the beginning?
Depends on how you set it up. In the absence of the actual commands you used,
there's no way to know whether you've positioned your molecule properly.
-Justin
Thanks,
On 8 July 2010 01:47, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
Please start new emails for new discussion topics. That way you
increase the chance that people with the interest and expertise can
use their time efficiently, and that you get an answer. Also,
archives work better if you separate topics.
> Please Let me ask two more simple questions about solvating a
molecule. I am using genbox to solvate a solute. I have solute.gro
and solvent.gro. What should be the dimension of box in solvent.gro
if i want to put -nmol numbers in the solute box. Does it matter
what size the box of solvent is (last line in gro)?
I don't think you are using the right tool for your problem, but
your description is so opaque it's hard to tell. genbox -nmol will
try to fill interstices, which need to exist for it to do any good.
That means you need to have prepared your solvent.gro with your
solute in mind.
> I have solvated the solute with 50 moleecules of solvent. I have
the structure file obtained from genbox. To run em or MD I need to
have top file. so I am using pdb2gmx and I get a top file for the
solute and 50 solvents but I have one moleculetype (named protein by
default). I am confused If I need to have 2 molecuels types for
solute and solvent, also if I need to enter the number of solvent
molecules at the end of the top file [mols] option, or what I have
now is fine and I can proceed to em and md usuing mdp files? :)
1. use pdb2gmx on an unsolvated .gro to get your protein .top
2. use editconf to set the simulation box how you want it
3. use genbox -p to add solvent and take care of modifying your .top
(unless your solvent is not water, in which case you'll probably
have to do some manual editing of your .top)
4. grompp and mdrun
Perhaps doing some tutorial material will make this and other
workflows more readily understood?
Mark
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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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