[gmx-users] Regarding em potential energy coming possitive

[Swagata Patra]

Thank you Justin for your reply.
So is it required to do more round of EM or should i proceed to NVT step?

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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-- 
Swagata Patra
M.Tech (Biotech)
JRF
IIT Guwahati