Re: [AMBER] questions about the input file of MD process

From: <asakiayumikio.gmail.com>
Date: Sun, 13 Mar 2011 08:04:28 -0700 (PDT)

hello, Carlos Simmerling!

thank you for your answer!

        2011-03-13
        
        asakiayumikio.gmail.com





发件人:Carlos Simmerling
发送日期:2011-03-13 22:38
收件人:AMBER Mailing List
抄送:
主题: Re: [AMBER] questions about the input file of MD process
pres0, like many other variables, can be set in the input file but if you do not set it the default value will be used. you can look in the output file to see what value amber is using- it reports the value whether you set it or not. 2011/3/13 <asakiayumikio@gmail.com> > hello, Francesco Oteri! > > Thank you for your answer. > > according to your reply, do you mean pres0 is a necessarity for equilibrium > simulation? > > 2011-03-13 > > asakiayumikio@gmail.com > > > > > > 发件人:Francesco Oteri > 发送日期:2011-03-13 22:27 > 收件人:amber@ambermd.org > 抄送: > 主题: Re: [AMBER] questions about the input file of MD process > Hi > > > while some in files neglect the pres0 and tempi parameters. > > > > my question is do we really need two parameters to carry out the > equilibrium simulation. > > > pres0 is the equilibrium pressure and it for this reason it is required > to run simulation in NPT ensemble. > tempi is the initial temperature used to assign the atomic velocities. > It is not strictly necessary to run constant-temperature MD because the > temperature is regulated by the temp0 parameter > > > _______________________________________________ > AMBER mailing list > AMBER@ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > . > _______________________________________________ > AMBER mailing list > AMBER@ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ AMBER mailing list AMBER@ambermd.org http://lists.ambermd.org/mailman/listinfo/amber
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Received on Sun Mar 13 2011 - 08:30:02 PDT
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