[gmx-users] Model of water

[Shima Arasteh]

As I studied in " Beyond modeling" by Peter Lai and coworkers, TIPS3P is the CHARMM variant of TIP3P, which TIPS3P recognizes additional van der waals interactions. So I guess I can use tips3p model of water instead of tip3p and go on. Correct? 

Then I need to know which model of water should be used in later simulations ( protein insertion in POPC) ? Is tips3p recommended?  

I'd like to know more about tips3p model. 

Thanks in advance.

 
Sincerely,
Shima


----- Original Message -----
From: Shima Arasteh <shima_arasteh2001 at yahoo.com>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Saturday, October 6, 2012 11:54 AM
Subject: Re: [gmx-users] Model of water



I tried to use genbox, but there is not tip3p.gro in GROMACS package, so spc216.gro is recommended to be used. I want to know what exactly I need to do to get the popc in water with tip3p model of water?

Thanks in advance.

Sincerely,
Shima


----- Original Message -----
From: Shima Arasteh <shima_arasteh2001 at yahoo.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Saturday, October 6, 2012 11:28 AM
Subject: [gmx-users] Model of water



 Dears, 

I got a link sent me by Peter Lai to simulate POPC in water: http://uab.hyperfine.info/~pcl/files/popc36/
He used TIP3SP, as it is apparent in its top file. I want to use simulate my own system of POPC in water with tip3p model of water? Is it possible to use its Peter's top and itp files? 

Please help me

Sincerely,
Shima
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