On 11/04/2012 4:13 AM, ramesh cheerla wrote:
Dear Mark,
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
editconf -f input.gro -o out_box1.gro -bt triclinic -box 3.22 2.608
7.792 -angles 90 125.4 90
it gave the following warning
WARNING: Triclinic box is too skewed.
for clarity here i am sending a part of the output file generated by
the editconf
God Rules Over Mankind, Animals, Cosmos and Such
6528
1PEGA C1 1 -0.025 0.408 -0.045
1PEGA C2 2 -0.015 0.326 0.084
::::::::::::::::::::::::::::::::::::::::::::::::::::::::;
3.22000 2.60800 6.35148 0.00000 0.00000 0.00000
0.00000 -4.51376 -0.00000
if i change the angles while using the editconf i observed the
following changes
editconf -f input.gro -o out_box2.gro -bt triclinic -box 3.22 2.608
7.792 -angles 90 90 125.4
Isn't that a totally different box? See editconf -h about -angles.
Mark
in this case editconf haven't given any warning and the output as follows
God Rules Over Mankind, Animals, Cosmos and Such
6528
1PEGA C1 1 1.477 0.167 0.675
1PEGA C2 2 1.487 0.085 0.804
::::::::::::::::::::::::::::::::::::::::::::::::::::::::;
3.22000 2.12585 7.79200 0.00000 0.00000 -1.51077
0.00000 -0.00000 -0.00000
Can you please help me in this regard.
thank you in advance.
On Mon, Ap;r 9, 2012 at 11:55 AM, Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>> wrote:
On 9/04/2012 3:22 PM, ramesh cheerla wrote:
Dear Gromacs users,
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.
So my box vector lengths are a = 3.22 nm, b = 2.608 nm, c =
7.792 nm.
I am using editconf to generate box for this crystal as:
editconf -f input.gro -o out_box.gro -bt tric -box 3.22 2.608
7.792 -angles 90 125.4 90
Here i have some doubts:
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
i haven't found any specific method for the generation of box
for the monoclinic crystal.
2) Is there any specific method to generate the box for the
monoclinic crystals.
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:
WARNING: Triclinic box is too skewed.
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.
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.
Mark
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