On 2010-08-31 21.19, Paymon Pirzadeh wrote:
Here is the command:
g_order_d_mpi -f 265K_50_50_50_2-pbcfixed.xtc -n wateroxygens.ndx -s
265K_50_50_50_2.tpr -o Sg265K
You need to replace -o by one of
-Sg sg-ang.xvg Output, Opt. xvgr/xmgr file
-Sk sk-dist.xvg Output, Opt. xvgr/xmgr file
-Sgsl sg-ang-slice.xvg Output, Opt. xvgr/xmgr file
-Sksl sk-dist-slice.xvg Output, Opt. xvgr/xmgr file
On Tue, 2010-08-31 at 21:15 +0200, David van der Spoel wrote:
On 2010-08-31 21.10, Paymon Pirzadeh wrote:
Yes,
I tried it, but I run into segmentation fault. Here is part of the error
message:
WARNING: distance between atoms 4869 and 0> 0.3 nm (3.515866). Index
file might be corrupt.
WARNING: distance between atoms 4870 and 0> 0.3 nm (3.580329). Index
file might be corrupt.
WARNING: distance between atoms 4871 and 0> 0.3 nm (3.489775). Index
file might be corrupt.
WARNING: distance between atoms 4872 and 0> 0.3 nm (3.464816). Index
file might be corrupt.
WARNING: distance between atoms 4873 and 0> 0.3 nm (3.561426). Index
file might be corrupt.
Segmentation fault
what command line are you using?
I thought it might be a periodic boundary issue, so I issued:
trjconv_d_mpi -f 265K_50_50_50_2.xtc -o 265K_50_50_50_2-pbcfixed -pbc
whole -s 265K_50_50_50_2.tpr
but the problem still persists. Any tips?
Regards,
Paymon
On Tue, 2010-08-31 at 20:37 +0200, David van der Spoel wrote:
On 2010-08-31 20.26, Paymon Pirzadeh wrote:
Hello,
It is said in the mannual that g_order compute the order parameter per
atom for carbon tails. Can it also calculate order (degree of
tetrahedrality) for water molecules if only water oxygens are selected
in index file? The reference paper is for water molecules though. Also,
does it calculate an average value or give a profile as a function of
time?
thanks,
Paymon
Have you tried it?
You can compute tetrahedrality for water, and also do it in slices
accross the box axis. It computes the average over time.
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell& Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell& Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
--
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