Re: [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 > 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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Re: [gmx-users] protein falls apart in energy minimization

[Zhong Zheng]

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?

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   
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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Re: [gmx-users] protein falls apart in energy minimization

[Pawan Kumar]

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  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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> Please search the archive at http://www.gromacs.org/search before posting!
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>
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Re: [gmx-users] protein falls apart in energy minimization

[Mark Abraham]

Zhong Zheng 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.


Are you seeing a visualization artefact caused by periodic boundary 
conditions? You can play with trjconv on your output file to see.


Mark
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[gmx-users] protein falls apart in energy minimization

[Zhong Zheng]

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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