Thanks for the reply.
I used cut=22.0 for saving conputer time, while I forget if I read
somewhere that cut=20.0 is used for such a simulation (and I choose a
better one, like cut=22.0). Will this setting introduce manifacts?
Jason said that "Seems like a good idea to me." I guess you didn't
think it is necessary to keep using LCPO and surften=0.00500. Am I
correct?
Huang
> Date: Fri, 15 May 2015 06:15:10 -0400
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Subject: Re: [AMBER] How to run GBSA in MD and binding energy
> calculation (MMPBSA.py)?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAGk3s-Q3Mba+7Zx7Hp-+5TGTJCmByUwXXQ2_6_k8=rGoqe2BLA.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Except that since gbsa=0 in the output, the surface area calculation is not
> done and not included in the forces. It is just telling you the default
> surften value, but it does not use it here.
> On May 15, 2015 5:08 AM, "Jason Swails" <jason.swails.gmail.com> wrote:
>
>> On Thu, May 14, 2015 at 11:46 PM, Huang <huangloligo.gmail.com> wrote:
>>
>> > I've run a simple MD with such an input:
>> > =============================================
>> > EQUILIBRATION
>> > &cntrl
>> > ntt=3, gamma_ln=5.0, ig=-1,
>> > nscm=1000, igb=5,
>> > saltcon=0.1, ntwx=1000, ntpr=100, temp0=298.0,
>> > nstlim=10000,rgbmax=20.0,cut=22.0,
>> > /
>> > &wt
>> > TYPE='END',
>> > /
>> >
>>
>> ?Is there any reason you're using a 22 A cutoff instead of an effectively
>> infinite one (like 1000)? For implicit solvent calculations, an infinite
>> cutoff is usually better.
>> ?
>>
>>
>> > =============================================
>> >
.......
>> ?
>>
>> > ??
>> > If I use the result mdcrd to run MMPBSA.py, should I keep using LCPO
>> > ??
>> > and surften=0.00500?
>> >
>> ??
>>
>> ?Seems like a good idea to me.?
>>
>> HTH,
>> Jason
>>
>> --
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Received on Mon Jun 15 2015 - 22:00:02 PDT
