[gmx-users] protein falls apart in energy minimization

[Justin A. Lemkul]

Zhong Zheng wrote:
> Thanks. That solves the problem. But I still see this warning message: 
> 
> Steepest Descents did not converge to Fmax < 10 in 201 steps.
> Potential Energy  = -1.2866480e+05
> Maximum force     =  3.4851584e+03 on atom 3683
> Norm of force     =  6.3128883e+01
> 
> That means I should run longer energy minimization until it converges 
> well and I don't see this error message. Is that right?

Maybe.  Are you still specifying nsteps = 2000 as in your original message?  If 
so, your machine has converged after 201 steps and you cannot necessarily force 
it to go longer.  You can change emtol and emstep, but you may or may not get a 
substantially different result in the end.  Also realize that Fmax < 10 is not 
often achieved in protein systems; Fmax < 1000 or < 100 is more common.

What you need to be looking at is what is causing the large force.  Look at the 
structure.  What is atom 3683?  Is it positioned too close to something else? 
Is there a geometric problem?

For the purposes of the archive, using -d should only be effective in resolving 
this issue if the box was set up improperly, leading to spurious forces between 
periodic images, if I understand the use of this "fix" correctly.  Was this the 
case in your system?

-Justin

> Thanks.
> 
> Zhong
> 
> On May 12, 2009, at 12:46 AM, Pawan Kumar wrote:
> 
>> hi,
>>
>> Defining a specific box size with -d option in editconf will help to 
>> overcome this problem...
>>
>> Regards,
>> Pawan
>>
>> On Tue, May 12, 2009 at 8:05 AM, Zhong Zheng <zhozheng at gmail.com 
>> <mailto:zhozheng at gmail.com>> wrote:
>>
>>     hi all
>>
>>     I am running Gromacs on a protein consisted of three chains. But
>>     no matter how I tried, the protein always falls into three parts
>>     (corresponding to each chain) after a simple 2000 steps energy
>>     minimization. Can anyone help me please? Thanks.
>>
>>     Zhong Zheng
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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