On 28/01/2011 3:44 PM, Makoto Yoneya wrote:
Dear Mark and all:
Dr. Mark Abraham wrote:
So you have to update the machinery that parses the .top to recognise
that the value of 4 is now legal.
and also
Did you set the environment variable to actually call the generic
nonbonded lists?
Thanks a
On 27/01/2011 12:11 PM, Makoto Yoneya wrote:
Dear Berk and all:
I'd tried to rewrite the routine
src/gmxlib/nonbonded/nb_generic.c
to modify the LJ potential to the shifted and truncated one.
First, I'd add the new switch(ivdw) as case 4, but when I'd tried;
[ defaults ]
; nbfunc comb-rule
Yes.
The pow function is expensive though. The code will run much faster
if you can use rinvsix, such as check for 2*rinvsix > c6/c12.
(I forgot the factor 2 in my previous mail).
Berk
> From: makoto-yon...@aist.go.jp
> To: gmx-users@gromacs.org
> Date: Tue, 11 Jan 2011 10:10:56 +0900
> Subjec
> From: makoto-yon...@aist.go.jp
> To: gmx-users@gromacs.org
> Date: Mon, 10 Jan 2011 23:57:46 +0900
> Subject: [gmx-users] truncated LJ potential
>
> Dear David and Hess:
>
> Thanks a lot for quick replies.
>
> >> please look into gromacs' table potential functionality, it is described
> >>
> Date: Mon, 10 Jan 2011 14:04:34 +0100
> From: sp...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] truncated LJ potential
>
> On 2011-01-10 13.39, Makoto Yoneya wrote:
> > Dear GROMACS experts:
> >
> > I'd like to use a m
On 2011-01-10 13.39, Makoto Yoneya wrote:
Dear GROMACS experts:
I'd like to use a modified Lennard-Jones potential (smoothly truncated at
only the repulsive part) in the following.
V(r)
= 4*epsilon*{ (sigma/r)^(12) - (sigma/r)^6 - (1/4) } for r<=
2^(1/6)*sigma
= 0 for r> 2^(1/6)*sigma
W
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