[gmx-users] Problem in energy minimization

[Jin J.C]

Dear Justin,
I have tried to change the box size, make it smaller a little, solvate
again and then, the error is resolved. Actually, I don't understand the
reason. especially, I have no idea about the "impossible geometry" as you
mentioned. Can you give me a little explanation?
Thank you so much.
Jin.

2015-06-04 20:38 GMT+09:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 6/3/15 10:23 PM, Jin J.C wrote:
>
>> Dear all,
>> I am trying to set a coarse-grained MD for the membrane protein.
>> After solvating, I met an error when running a short energy minimization (
>> 10 steps) before adding ions.
>>
>> Steepest Descents:
>> Tolerance (Fmax)   =  1.00000e+01
>> Number of steps    =           10
>> Step=   10, Dmax= 2.0e-05 nm, Epot=  2.76192e+20 Fmax=         inf, atom=
>> 8872
>> Reached the maximum number of steps before reaching Fmax < 10 writing
>> lowest energy coordinates.
>> Steepest Descents did not converge to Fmax < 10 in 11 steps.
>> Potential Energy  =  2.7619190e+20
>> Maximum force    =           inf on atom 8872
>> Norm of force       =            inf
>>
>> The reason is because of Maximum force is equal to infinity. Therefore I
>> can not proceed further. Atom 8872 is water atom. Even when I delete this
>> atom, the error occurs again with another water molecules, and goes on.
>>
>> Can someone help me figure out? and explain to me what happen?  Is this
>> because of overlapping problem?
>>
>>
> Likely.  You have some impossible geometry somewhere, or otherwise
> something is very wrong with the topology.
>
> -Justin
>
> --
> ==================================================
>
> 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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