AMBER Archive (2004)

Subject: Re: AMBER: MD after partially solvated

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Sat Oct 30 2004 - 22:11:27 CDT

read the section of the manual about temperature control. NTB relates to
box and periodicity,
and NTT relates to thermostats. these are different things.

===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

Xiao He wrote:

>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
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>.
>>
>>
>
>= = = = = = = = = = = = = = = = = = = =
>
>
>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ÖÂ
>Àñ£¡
>
>
>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡Xiao He
>
>
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