On 11/9/13 11:37 AM, rajat desikan wrote:
Hi Justin,
1) I am doing all three. -type x, -type y, -lateral z (xy) ...(I am looking
at anisotropy in dynamics if any)
2) Yes, 192 phosphate beads is exact. I have 384 lipids in my system
(192/leaflet)
If you were to remove the COM motion of individual leaflets and extract the
MSD, what would you do? Do you see any error in my workflow?
Thanks. Appreciate any suggestions...
What you did looks reasonable to me. Seg faults are frustrating, but can only
really be addressed by recompiling in debug mode and running the command through
a debugger to see which function is failing.
-Justin
On Sat, Nov 9, 2013 at 7:16 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 11/9/13 5:24 AM, rajat desikan wrote:
Hi All,
I have a few older membrane simulations for which the COM for the upper
and
lower leaflets were not removed in the course of the simulations. These
are
pretty long simulations exceeding 300 ns.
I have trouble with post-processing of the trajectory.
To remove the COM of the upper and lower leaflets separately, I executed
the following series of commands (shown for upper only):
Selecting upper leaflet:
g_select -s .tpr -on upper_P8.ndx -select 'resname DPPC and name P8 and
res_com z>4.3'
trjconv -f .gro -s .gro -n upper_P8.ndx -o test_u_P8.pdb .........Testing
selection, everthing ok
Trajectory:
trjconv -f .xtc -s .tpr -n upper_P8.ndx -o upperP8_center_pbcnojump.xtc
-center -b 20000 -pbc nojump
MSD:
g_msd -f upperP8_center_pbcnojump.xtc -s .tpr -o msd_dppc_x_u.xvg -type x
-n upper_P8.ndx
You probably want the -lateral option as well.
Select a group to calculate mean squared displacement for:
Group 0 (resname_DPPC_and_name_P8_and_res_com_z>4.3_0.000) has 192
elements
Does the fact that there are 192 identified P8 atoms match your
expectations for this membrane?
-Justin
There is one group in the index
Reading frame 60 time 20600.000 Segmentation fault (core dumped)
Any ideas? Is there anything wrong with my workflow?
Thanks.
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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