Re: [gmx-users] How to modify code so that rlist > rcoulomb

Tue, 22 Jul 2008 13:19:02 -0700

Berk,

Thanks for the link to discussion related to the same topic. It was really helpful in understanding the details of implementation and what options are suitable.

What I meant by shifting the potential was that the potential is changed from the original form. From gromacs manual,

"There is no fundamental difference between a switch function (which multiplies the potential with
a function) and a shift function (which adds a function to the force or potential)"

Thanks,
Jeetain

Berk Hess wrote:
Hi,

PME-switch does not shift, it only switches.
It does not make sense to use plain PME with a cut-off,
but also this in impossible with the way the Gromacs innerloops work.
For a detailed (and long) discussion on this topic see:
http://bugzilla.gromacs.org/show_bug.cgi?id=196

Berk.


From: [EMAIL PROTECTED]
To: [email protected]
Date: Mon, 21 Jul 2008 16:00:26 -0400
Subject: [gmx-users] How to modify code so that rlist > rcoulomb

Hi Berk,

Thanks for your response. I am trying to simulate the following options,

ns_type         = grid
rlist                = 3.2
coulombtype = pme
rcoulomb       = 1.0
vdw-type        = cut-off
rvdw               = 3.0
fourierspacing  = 0.12
pme_order       = 4
ewald_rtol      = 1e-5
optimize_fft    = yes

I tried the following with gromacs 3.3.99_development_200800503,

ns_type         = grid
rlist                = 3.2
coulombtype = pme-switch
rcoulomb       = 1.0
rcoulomb_switch = 0.0
vdw-type        = shift
rvdw               = 3.0
rvdw_switch   = 0.0
fourierspacing  = 0.12
pme_order       = 4
ewald_rtol      = 1e-5
optimize_fft    = yes

and it works. I want something similar to PME-Switch (rlist > rcoulomb) but without shifting the real space coulomb part.  Is this possible? When I try the option rcoulomb_switch > rcoulomb, it gives an error.

Thanks,
Jeetain

> Hi,

> You did not specify for which type of vdw and electrostatics you want this option.
> For plain cut-off's it does not make sense.
> In version 3.3 you can do what you want with the shift and switch options.
>
> In the CVS version there are also Reaction-Field-zero and PME-Switch.
>
> Berk.


> From: jeetain at gmail.com
> To: gmx-users at gromacs.org
> Date: Sat, 19 Jul 2008 16:38:59 -0400
> Subject: [gmx-users] How to modify code so that rlist > rcoulomb
> 
> Hi All,
> 
> I want to simulate a system for which rvdw > rcoulomb and to account  
> for LJ interactions correctly rlist should be greater than rvdw (if  
> nstist != 1). For current gromacs setup rlist should be equal to  
> rcoulomb. I searched the mailing list and there has been several  
> discussions related to this issue such as,
> 
> http://www.gromacs.org/pipermail/gmx-users/2006-July/022804.html
> 
> I was wondering if anyone has implemented something already so that a  
> system with,  rlist > rvdw > rcoulomb, can be simulated without any  
> problem. Can anyone please guide me what files / variables should be  
> changed to implement this.
> 
> Thanks,
> Jeetain 
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