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On 9/07/2010 12:59 PM, jojo J wrote:
<blockquote
cite="mid:AANLkTinTFa859912Hec3WQgk2PT8Ta0nbVCmW0lxuInY@mail.gmail.com"
type="cite">Hello Mark,<br>
<br>
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)<br>
</blockquote>
<br>
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.<br>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTinTFa859912Hec3WQgk2PT8Ta0nbVCmW0lxuInY@mail.gmail.com"
type="cite"><br>
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? <br>
<br>
Thanks,<br>
<br>
<div class="gmail_quote">On 8 July 2010 01:47, Mark Abraham <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">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.<br>
<br>
<font
style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">>
</font>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)?<br>
<br>
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.<br>
<br>
<font
style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">>
</font>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? :)<br>
<br>
1. use pdb2gmx on an unsolvated .gro to get your protein .top<br>
2. use editconf to set the simulation box how you want it<br>
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)<br>
4. grompp and mdrun<br>
<br>
Perhaps doing some tutorial material will make this and other workflows
more readily understood?<br>
<font color="#888888"><br>
Mark </font><br>
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</blockquote>
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