Dear Mark,
Once again I am very thankful to you for your reply, I
have extracted box vectors from .XTC file by using g_traj with -ob
option with this I was able to get only six vector components viz XX
YY ZZ YX ZX and ZY only how about remaining three vector components
XY XZ
Dear Gromacs users,
I am using gromacs for simulations of a polymer, for that I
am planing to see how lattice parameters a , b c are varying
during simulation. Here lattice parameter a is the length of unit
cell along X- direction, b is the length of the unit cell along
Y axis and c
On 16/08/2012 5:46 AM, ramesh cheerla wrote:
Dear Gromacs users,
I am using gromacs for simulations of a polymer, for that I
am planing to see how lattice parameters a , b c are varying
during simulation. Here lattice parameter a is the length of unit
cell along X- direction, b
Dear Mark,
Thank you for your reply, as you suggested I will go
through the sec 7.4 and 8 of the manual and moreover how would I get
exact box vectors XX YY ZZ XY XZ YX YZ ZX ZY for each frame of
trajectory in gromacs
As I am new to gromacs I have no Idea where these will be
On 16/08/2012 3:22 PM, ramesh cheerla wrote:
Dear Mark,
Thank you for your reply, as you suggested I will go
through the sec 7.4 and 8 of the manual and moreover how would I get
exact box vectors XX YY ZZ XY XZ YX YZ ZX ZY for each frame of
trajectory in gromacs
They're in
On Thu, Dec 8, 2011 at 12:33 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 8/12/2011 2:54 PM, Chandan Choudhury wrote:
Thanks everyone for the responses. I should have framed my question much
more precisely. I am trying to use the template.c code of (gmx_4.0.7) and
within this, I want
On 9/12/2011 12:00 AM, Chandan Choudhury wrote:
On Thu, Dec 8, 2011 at 12:33 PM, Mark Abraham mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au wrote:
On 8/12/2011 2:54 PM, Chandan Choudhury wrote:
Thanks everyone for the responses. I should have framed my
question much
Hey,
On a general note, assuming the frame is read in as a t_trxframe
structure called frame, the box is accessible as frame.box and is a
matrix instance, which means it's a 3x3 array, containing the
triclinic box as a lower triangular matrix. If the code says
t_trxframe *frame somewhere, rather
Dear gmx_users,
I am using gmx_4.0.7. I need to print the box vectors from the trajectory
of a simulated system. How can this be achieved? Can someone help me out?
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
--
gmx-users mailing listgmx-users@gromacs.org
#!/usr/bin/env python
# Python compliant email -- Just save the content :)
Hey :)
The neatest way is using python to extract them from the XTC file :)
from struct import unpack
import sys
import os
def i(x): return sum([ord(x[j])(24-j*8) for j in range(4)])
def
Impressive :)
On Wed, Dec 7, 2011 at 1:34 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
#!/usr/bin/env python
# Python compliant email -- Just save the content :)
Hey :)
The neatest way is using python to extract them from the XTC file :)
from struct import unpack
import sys
On 8/12/2011 4:36 AM, Chandan Choudhury wrote:
Dear gmx_users,
I am using gmx_4.0.7. I need to print the box vectors from the
trajectory of a simulated system. How can this be achieved? Can
someone help me out?
g_energy on the .edr file (assuming that the vectors actually vary).
Mark
--
Thanks everyone for the responses. I should have framed my question much
more precisely. I am trying to use the template.c code of (gmx_4.0.7) and
within this, I want to take care of PBC. To do this, I should be having the
knowledge of box dimensions. How can this done?
I also know that the
On 8/12/2011 2:54 PM, Chandan Choudhury wrote:
Thanks everyone for the responses. I should have framed my question
much more precisely. I am trying to use the template.c code of
(gmx_4.0.7) and within this, I want to take care of PBC. To do this, I
should be having the knowledge of box
Makoto Yoneya wrote:
Dear GROMACS users:
I found the following in ML archive about the box vectors entry in gro
file.
doing:
% editconf -f in.pdb -o out.gro -bf tric -box a b c -angles bc ac
ab
the last line of out.gro looks like:
1.12020 0.92620 6.259008 0.0 0.0 0.0 0.0
Hi David/Makoto,
I wouldn't call it a stupid error, keeping nine numbers for the
definition of a box. Of course in simulation the lower triangular part
of the box matrix is zero. But if you reorient the system and want to
preserve PBC (like after fitting), the box will be rotated and the
full
Dear GROMACS users:
I found the following in ML archive about the box vectors entry in gro
file.
doing:
% editconf -f in.pdb -o out.gro -bf tric -box a b c -angles bc ac
ab
the last line of out.gro looks like:
1.12020 0.92620 6.259008 0.0 0.0 0.0 0.0 -0.99134
0.0
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