From: bharat gupta (bharat.85.monu_at_gmail.com)
Date: Tue Jul 05 2011 - 03:40:59 CDT
I repeated the nvt equilibration again with cell origin (the actual one),
but still I am getting the protein going out of the box. But the energy and
temperature is stable. What shall I do in this case, shall I continue with
npt simulation without keeping the protein in the center of the box as I
have taken PBC into consideratioon ???
On Tue, Jul 5, 2011 at 3:22 PM, bharat gupta <bharat.85.monu_at_gmail.com>wrote:
> The system is too hot ??... but I checked the temperature column was empty
> as I kept temperature control settings. Now I am repeating it again with
> some different settings earlier I gave 0 0 0 for cell origin , now I have
> given the correct values. After this npt .
>
> After npt , I have to simulate my system for 10ns in that case only free
> dynamics without temp and pressure control will be fine ??
>
>
> On Tue, Jul 5, 2011 at 3:15 PM, Norman Geist <
> norman.geist_at_uni-greifswald.de> wrote:
>
>> Only if it is unusual that your protein moves that much. Then maybe
>> your system is to hot or something. But it can just be normal and has no
>> effect because its periodic.****
>>
>> ** **
>>
>
>
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010_at_yahoo.com
>
>
-- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46010_at_yahoo.com
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