AMBER Archive (2004)

Subject: AMBER: MD after partially solvated

From: Xiao He (hx_at_itcc.nju.edu.cn)
Date: Sat Oct 30 2004 - 21:52:51 CDT

Dear Amber users,

I used partially solvated like 'solvateCap test WATBOX216 { 1 -37 21 } 22'.
I'm now doing 'step 1 Heating up the system then MD under Constant pressure and constant temperature '
Is it possible to keep constant tempature in MD after heating to 300K from 100K?
Since there are no box informations in partially solvated system ,so 'NTB=1 and NTB=2' can not be used.
How to set the parameters in sander.Thanks a lot!

He Xiao

>Hello Xiao,
>
>You need to have solvent box for doing the contant pressure and constant
>volume MD. For that you need to solvate your solute using solvatebox OR
>solvateoct in xleap/tleap. Solvateoct is better choice. The best way to
>start amber is see the examples distributed along with amber7 or 8. Usually
>constant volume MD for about 50ps is performed prior to contant pressure MD
>in order to avoid large changes in system due large velocities at the
>beginning of MD.
>
>I hope it helps,
>
>Jiten
>
>----- Original Message -----
>From: "Xiao He" <hx_at_itcc.nju.edu.cn>
>To: "Jiten" <jiten_at_postech.ac.kr>
>Sent: Saturday, October 30, 2004 5:57 PM
>Subject: amber question
>
>
>> Hi,Jiten
>> I want to keep constant temperature in MD simulation,but non-periodical
>> condition ,so I can't use ntb=2,
>> then how to set in sander?
>> Thanks!
>> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡Xiao He
>> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡hx_at_itcc.nju.edu.cn
>> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2004-10-30
>>
>>
>>
>>
>>
>
>.

= = = = = = = = = = = = = = = = = = = =
                        

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¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡Xiao He
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡hx_at_itcc.nju.edu.cn
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2004-10-30

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