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

[Justin Lemkul]

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

==================================================