Dear Mark and all:
Dr. Mark Abraham wrote:
> > and set the environment variable?
>
> You'd only have learned to do this if you'd used a debugger to step
> through the flow of the code. I highly recommend that procedure.
> init_forcerec() checks an environment variable and triggers the use of
>
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
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 lot for your comments.
I did not care t
ix, such as check for 2*rinvsix> c6/c12.
(I forgot the factor 2 in my previous mail).
Berk
From: makoto-yoneya at aist.go.jp
To: gmx-users at gromacs.org
Date: Tue, 11 Jan 2011 10:10:56 +0900
Subject: [gmx-users] truncated LJ potential
Dear Berk:
Thanks again for the further reply.
The LJ pot
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-yoneya at aist.go.jp
> To: gmx-users at gromacs.org
> Date: Tue, 11 Jan 2011 10:1
:10:56 +0900
> Subject: [gmx-users] truncated LJ potential
>
> Dear Berk:
>
> Thanks again for the further reply.
>
> >> The LJ potential and force code in the above looks like in the c6-c12
> form
> >> not in epsilon-sigma one.
> >> The LJ potential modi
Dear Berk:
Thanks again for the further reply.
>> The LJ potential and force code in the above looks like in the c6-c12
form
>> not in epsilon-sigma one.
>> The LJ potential modification I'd like to try is based on the epsilon-
>> sigma form and the mixing rule is the Lorents-Bertelot's one.
>> C
> 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
Dear David and Hess:
Thanks a lot for quick replies.
>> please look into gromacs' table potential functionality, it is described
>> in the manual, and you won't have to program anything
>> UNLESS the sigma is different for different atom pairs, in that case I'm
>> not sure if it will work.
The
> 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
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
Which routine should I change to realize this
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