[gmx-users] Trouble calculating MSD after removing COM for upper and lower leaflets

[rajat desikan]

Hi Justin,
Thanks for your time. I think I will use g_traj to spit out the P8
coordinates from upperP8_center_pbcnojump.xtc and write my own little MSD
routine :)



On Sat, Nov 9, 2013 at 11:36 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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 <jalemkul at 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
>>>
>>> jalemkul at 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
> ==================================================
> --
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-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore