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On 11/04/2012 4:13 AM, ramesh cheerla wrote:
<blockquote
cite="mid:CAPNFZqeYrnw=FaWmtAmpJeNKWrquTO8H6ZaewBrCiUP4ceSHtw@mail.gmail.com"
type="cite">Dear Mark,<br>
<br>
Thank you for reply, sorry for not being very clear,
Here my doubt is can i use triclinic box for the simulations of
the crystal whose unit cell is monoclinic. As i said earlier i
have tried editconf as <br>
editconf -f input.gro -o out_box1.gro -bt triclinic -box 3.22
2.608 7.792 -angles 90 125.4 90<br>
it gave the following warning <br>
<br>
WARNING: Triclinic box is too skewed.<br>
<br>
for clarity here i am sending a part of the output file generated
by the editconf<br>
God Rules Over Mankind, Animals, Cosmos and Such<br>
6528<br>
1PEGA C1 1 -0.025 0.408 -0.045<br>
1PEGA C2 2 -0.015 0.326 0.084<br>
::::::::::::::::::::::::::::::::::::::::::::::::::::::::;<br>
3.22000 2.60800 6.35148 0.00000 0.00000 0.00000
0.00000 -4.51376 -0.00000<br>
if i change the angles while using the editconf i observed the
following changes<br>
<br>
editconf -f input.gro -o out_box2.gro -bt triclinic -box 3.22
2.608 7.792 -angles 90 90 125.4<br>
</blockquote>
<br>
Isn't that a totally different box? See editconf -h about -angles.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAPNFZqeYrnw=FaWmtAmpJeNKWrquTO8H6ZaewBrCiUP4ceSHtw@mail.gmail.com"
type="cite">
in this case editconf haven't given any warning and the output as
follows <br>
<br>
God Rules Over Mankind, Animals, Cosmos and Such<br>
6528<br>
1PEGA C1 1 1.477 0.167 0.675<br>
1PEGA C2 2 1.487 0.085 0.804<br>
::::::::::::::::::::::::::::::::::::::::::::::::::::::::; <br>
3.22000 2.12585 7.79200 0.00000 0.00000 -1.51077
0.00000 -0.00000 -0.00000<br>
<br>
Can you please help me in this regard.<br>
<br>
thank you in advance.<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<div class="gmail_quote">On Mon, Ap;r 9, 2012 at 11:55 AM, 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="margin:0pt 0pt 0pt
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class="HOEnZb">
<div class="h5">On 9/04/2012 3:22 PM, ramesh cheerla wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
Dear Gromacs users,<br>
<br>
I am planing to simulate a
polymeric crystal in gromacs, which is of monoclinic
unit cell with cell parameters a = 0.805 nm b = 1.304 nm
and c = 1.948 nm and beta = 125.4 deg. my crystal is of
424 type i.e 4 unit cells along 'a' direction '2' unit
cells along 'b' direction and 4 unit cells along 'c'
direction.<br>
So my box vector lengths are a = 3.22 nm, b = 2.608 nm,
c = 7.792 nm.<br>
I am using editconf to generate box for this crystal
as:<br>
<br>
editconf -f input.gro -o out_box.gro -bt tric -box 3.22
2.608 7.792 -angles 90 125.4 90<br>
<br>
Here i have some doubts:<br>
<br>
1) Am i using the editconf in correct manner for
generation of box for the monoclinic crystal, though the
crystal is of monoclinic i am using box type as
triclinic<br>
i haven't found any specific method for the generation
of box for the monoclinic crystal.<br>
2) Is there any specific method to generate the box for
the monoclinic crystals.<br>
3) The notations for the lattice parameters of the
crystal i.e 'a' , 'b' , 'c' and angles alpha, beta ,
gamma used by crystallography and the gromacs editconf
are the same or different, why because if i use editconf
as above i am getting the following warning:<br>
<br>
WARNING: Triclinic box is too skewed.<br>
</blockquote>
<br>
</div>
</div>
This means equation 3.3 of the manual is not true. Maybe beta
should be acute? I've no idea of necessity or convention here.<br>
<br>
Inspecting the whole output of editconf is probably
instructive, but you've kept all that information to yourself
instead of re-thinking how your repeat post might be
constructed so as to make it easier / more likely for people
help you. Likewise the final line of out_box.gro. Make sure
you have read and understood what documentation is available
with editconf -h and in manual section 3.2.<span
class="HOEnZb"><font color="#888888"><br>
<br>
Mark<br>
-- <br>
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</font></span></blockquote>
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