[gmx-users] Model of water

[Shima Arasteh]

Thanks for your explanation.
Do you mean genbox will adapt the model and the force field automatically? 


Sincerely,
Shima


----- Original Message -----
From: Peter C. Lai <pcl at uab.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>
Cc: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Saturday, October 6, 2012 3:27 PM
Subject: Re: [gmx-users] Model of water

I used TIPS3P in everything, because after all, it's CHARMM's water and
no reviewer can complain about using it with CHARMM. If you want a faster 
simulation you can try using the regular TIP3P and see if the bilayer metrics 
remain satisfactory for you. If you still have doubts, run simulations with 
both TIPS3P and TIP3P and decide if the differences are significant. IIRC 
Thomas Piggot's latest CHARMM36 Gromacs paper "Molecular Dynamics Simulations 
of Phosphatidylcholine Membranes: A Comparative Force Field Study" has some 
results on POPC in TIP3P vs. TIPS3P.

When using genbox, you always use spc216.gro as the starting solvent 
coordinates. The waters will adopt the correct physical properties specified 
by the model and forcefield during equilibration.

On 2012-10-06 02:40:58AM -0700, Shima Arasteh wrote:
> 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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-- 
==================================================================
Peter C. Lai            | University of Alabama-Birmingham
Programmer/Analyst        | KAUL 752A
Genetics, Div. of Research    | 705 South 20th Street
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