[gmx-users] Energy minimization has stopped....

[Justin Lemkul]

On 11/5/13 7:31 AM, Kalyanashis Jana wrote:
> Dear Justin,
>    Can you please tell me, how I can solve this problem?? If I will change
> the coordinate of atom 15461, will it help me? But you know, I did this
> step changing the position of drug molecule and I got same error.
>

You should first do what I suggested before.  The reason for a large force is 
either (1) bad atomic clashes that should be apparent upon visual inspection or 
(2) bad topology for the drug.

-Justin

>
> On Tue, Nov 5, 2013 at 5:44 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 11/5/13 6:28 AM, Kalyanashis Jana wrote:
>>
>>> Hi,
>>>     Whenever I am trying to do position retrained MD run, It has been
>>> stopped
>>> at middle of the MD run. I have given the following error. Can you please
>>> suggest me something to resolve this error?
>>> Energy minimization has stopped, but the forces havenot converged to the
>>> requested precision Fmax < 100 (whichmay not be possible for your system).
>>> It
>>> stoppedbecause the algorithm tried to make a new step whose sizewas too
>>> small, or there was no change in the energy sincelast step. Either way, we
>>> regard the minimization asconverged to within the available machine
>>> precision,given your starting configuration and EM parameters.
>>>
>>> Double precision normally gives you higher accuracy, butthis is often not
>>> needed for preparing to run moleculardynamics.
>>>
>>> writing lowest energy coordinates.
>>>
>>> Steepest Descents converged to machine precision in 20514 steps,
>>> but did not reach the requested Fmax < 100.
>>> Potential Energy  = -9.9811250e+06
>>> Maximum force     =  6.1228135e+03 on atom 15461
>>> Norm of force     =  1.4393512e+01
>>>
>>>
>> Visualize the output, specifically near atom 15461.  The forces there are
>> too high and cannot be resolved further.  Any attempt to use these
>> coordinates for dynamics will probably lead to a crash.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> 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
>>
>> ==================================================
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>

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

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

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