[gmx-users] Regarding em potential energy coming possitive

[Justin Lemkul]

On 9/28/16 9:03 PM, Swagata Patra wrote:
> Thank you so much for clarifying my doubt.
>
> But why potential energy coming so high? Is it because Fmax<1?
>

There's nothing abnormal about your potential energy.  It's also not "high" 
because it's a negative number, exactly in the range where you would expect an 
average-sized, solvated protein system.

-Justin

> On Thu, Sep 29, 2016 at 6:29 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 9/28/16 8:57 PM, Swagata Patra wrote:
>>
>>> Thank you Justin for your reply.
>>> So is it required to do more round of EM or should i proceed to NVT step?
>>>
>>>
>> If this is just normal MD, yes.  There's no need to try to get Fmax < 1
>> for that.
>>
>> -Justin
>>
>>
>> On Thu, Sep 29, 2016 at 6:23 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>>
>>>> On 9/28/16 8:50 PM, Swagata Patra wrote:
>>>>
>>>> Hello everyone,
>>>>>
>>>>> I am facing a problem in energy minimization step. I am not sure if the
>>>>> system is energy minimized or not. After completing the em, I am getting
>>>>> the following message:
>>>>> Reached the maximum number of steps before reaching Fmax < 1
>>>>>
>>>>> Steepest Descents did not converge to Fmax < 1 in 100001 steps.
>>>>> Potential Energy  = -9.38185842721980e+06
>>>>> Maximum force     =  4.73530543550372e+02 on atom 1694
>>>>> Norm of force     =  1.11096437377417e+00
>>>>> But when I am calculating the potential energy getting the following
>>>>> message:
>>>>> Energy                      Average   Err.Est.       RMSD  Tot-Drift
>>>>> ------------------------------------------------------------
>>>>> -------------------
>>>>> Potential                   121.811    1.9e+06        nan   -2017.89
>>>>>  (kJ/mol)
>>>>>
>>>>> Potential energy should come negative. But here its too high.
>>>>> One more thing that I want to tell is, in my protein pdb file there is
>>>>> gap
>>>>> between amino acids(like G229 then H412). That's why in topology file I
>>>>> am
>>>>> getting two chains.
>>>>> Please suggest me what could be the problem?
>>>>>
>>>>>
>>>>> I don't see a problem.  The energy is fine and the maximum force is fine
>>>> for most purposes.  You only need to achieve Fmax < 1 for NMA, but to do
>>>> so
>>>> you probably need a few rounds of EM, not just a single run of steepest
>>>> descents.
>>>>
>>>> -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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>>>
>>>
>>>
>> --
>> ==================================================
>>
>> 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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>
>
>

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

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

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