[gmx-users] segmentation fault with unusually high temperature and energy values

[Justin Lemkul]

On 10/5/16 6:12 AM, Sahithya S Iyer wrote:
> Hi gmx users,
>
> I am trying to set up a membrane protein system. The protein has to be at a
> specific location of the heterogeneous bilayer patch (hence i cannot use
> inflateGRO.py) to set up the system. I used vmd to place the protein and
> remove overlapping lipid ("within 3 of protein"). There are no overlapping
> molecules in my system now.
>
> When i try to energy minimize this system, the simulation crashes with
> segmentation error. The log files shows abnormally high energy and
> temperature values -
>

If you have a temperature, then you're not actually energy-minimizing anything; 
this is the output of a dynamics run.

Note the absolute insanity of all the values; your system is hotter than the 
surface of the sun by a factor of nearly 10^29.  Likely your system has severe 
clashes or the topology is otherwise unsound.

-Justin

> Grid: 25 x 24 x 7 cells
> Large VCM(group rest): 219789.21875, -46415.75391, -69344.71094, Temp-cm:
> 2.55463e+12
>    Energies (kJ/mol)
>            Bond       G96Angle  Improper Dih.        LJ (SR)   Coulomb (SR)
>     9.44989e+07    1.67042e+05    1.96681e+04    1.59212e+18   -2.29853e+05
>  Position Rest.      Potential    Kinetic En.   Total Energy    Temperature
>     3.58499e+02    1.59212e+18    2.35242e+35    2.35242e+35    3.00779e+32
>  Pressure (bar)   Constr. rmsd
>     4.60453e+32    5.67792e+13
>
> When i visualize the trajectroy, in the second frame, the atoms are
> scattered all over outside the box !
> I have run the lipid patch and protein system (separately) individually and
> it runs fine without any error.
>
> Can someone please tell me where i am going wrong..
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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