Re: [gmx-users] Minimization error

2011-10-19 Thread Mark Abraham 

On 20/10/2011 4:14 PM, aiswarya pawar wrote:

Hi,

All the parameters are ok, still i get the complex separated.


Simulation parameters have nothing to do with the phenomena in the FAQ 
Justin pointed out to you. Please read it.


Mark




On Wed, Oct 19, 2011 at 7:02 PM, Justin A. Lemkul > wrote:




aiswarya.pa...@gmail.com  wrote:

Hi Users,

I performed a simple minimization for a protein complex in
vacuum. Didn't get any error while performing the minimization
but when visualised the pdb file after the minimization the
chains of the protein complex separated.

What could be the reason.


Please see FAQ #3 under the heading:

http://www.gromacs.org/Documentation/FAQs#Analysis_and_Visualization

-Justin


Thanks,
Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's
No. 1 Network. Go for it!


-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Minimization error

2011-10-19 Thread aiswarya pawar 
Hi,

All the parameters are ok, still i get the complex separated.


On Wed, Oct 19, 2011 at 7:02 PM, Justin A. Lemkul  wrote:

>
>
> aiswarya.pa...@gmail.com wrote:
>
>> Hi Users,
>>
>> I performed a simple minimization for a protein complex in vacuum. Didn't
>> get any error while performing the minimization but when visualised the pdb
>> file after the minimization the chains of the protein complex separated.
>>
>> What could be the reason.
>>
>>
> Please see FAQ #3 under the heading:
>
> http://www.gromacs.org/**Documentation/FAQs#Analysis_**and_Visualization
>
> -Justin
>
>
>  Thanks,
>> Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1
>> Network. Go for it!
>>
>>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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] Minimization error

2011-10-19 Thread Justin A. Lemkul 



aiswarya.pa...@gmail.com wrote:

Hi Users,

I performed a simple minimization for a protein complex in vacuum. Didn't get 
any error while performing the minimization but when visualised the pdb file 
after the minimization the chains of the protein complex separated.

What could be the reason.



Please see FAQ #3 under the heading:

http://www.gromacs.org/Documentation/FAQs#Analysis_and_Visualization

-Justin


Thanks,
Aiswarya 
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Minimization error

2011-10-19 Thread mu xiaojia 
1 check with the rtp files in your forcefield, especially the parameters
2 check with the imput pdb file, the format matters a lot.


On Wed, Oct 19, 2011 at 8:18 AM,  wrote:

> Hi Users,
>
> I performed a simple minimization for a protein complex in vacuum. Didn't
> get any error while performing the minimization but when visualised the pdb
> file after the minimization the chains of the protein complex separated.
>
> What could be the reason.
>
> Thanks,
> Aiswarya
> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for
> it!
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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[gmx-users] Minimization error

2011-10-19 Thread aiswarya . pawar 
Hi Users,

I performed a simple minimization for a protein complex in vacuum. Didn't get 
any error while performing the minimization but when visualised the pdb file 
after the minimization the chains of the protein complex separated.

What could be the reason.

Thanks,
Aiswarya 
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- 
gmx-users mailing listgmx-users@gromacs.org
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