On 9/07/2010 12:59 PM, 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)
Your conception of the workflow seems a bit confused. If you want to
minimize your initial configuration before replication, then it is best
to do that with an .mdp file that turns off PBC. Some reading in section
7.3 of the manual will (eventually) let you see how to do that - and
what you don't need to know right now will be useful later.
Alternatively, make the box size large enough now, do EM.
Then, with the post-minimization structure, pick a box size suitable for
replication, then use genconf. Then, do whatever you want to do with the
replicated structure.
Mark
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?
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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