[gmx-users] Regarding em potential energy coming possitive
swagataliza at gmail.com
Thu Sep 29 02:57:46 CEST 2016
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
>> Energy Average Err.Est. RMSD Tot-Drift
>> Potential 121.811 1.9e+06 nan -2017.89
>> 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
> 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
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