AMBER Archive (2009)

Subject: Re: [AMBER] part of the protein escaped from the water box

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Oct 15 2009 - 06:39:40 CDT

Not a problem. Use ptraj center and image commands if you want to
analyze wate on the protein surface. Check the archives for details.

On Oct 15, 2009, at 7:33 AM, "qiaoyan" <qiaoyan_at_dicp.ac.cn> wrote:

>
> Dear everyone:
> I simulate a protein including 104 residues, the protein was
> surrounded by a periodic box of water molecules described by the
> TIP3P potential extended to a distance of 10.0A from any solute
> atom. After 6ns of constant-pressure simulation, part of the protein
> escaped from the waterbox, I don't know whether this phenomenon
> affect the result, please help me,thank you!
> The script I use is as follows:
> &cntrl
> imin=0,
> ntx=5, irest=1,
> ntpr=100, ntwx=1000,ntwr=5000,
> dt=0.002,nstlim=1000000, nscm=1000,
> cut=9.,dielc=1.0,iwrap=1.0,
> ntc=2, ntf=2,
> ntb=2,
> ntp=1,pres0=1.0,taup=3.0,
> ntt=1, tautp=3.0,temp0=300.0,
> ioutfm=1
> /
> Have a nice day!
>
> qiaoyan
>
> 2009-10-15
>
>
>
> qiaoyan
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