st for GROMACS users
Subject: Re: [gmx-users] modify C6 directly in FF using sigma and
epsilon
David Mobley wrote:
> David,
>
> I'm using 3.3/3.3.1.
>
> Is there an easy tweak to the source code that would allow something
> like this? i.e. could I somehow easily tweak
://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel
Sent: Friday, April 06, 2007 4:11 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] modify C6 directly in FF using sigma and
epsilon
David
-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of David Mobley
Sent: Friday, April 06, 2007 2:20 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] modify C6 directly in FF using sigma and epsilon
Gromacs users,
I'm using a force field (the port of AMBER to GR
David,
It seems that your best bet is to write that little Perl script to
convert the whole force field to C6/C12.
It's a little worse than that, since I still need to use the same
combination rules. I'll have to create a new "force field" where I
define all possible pairs of nonbonded interac
David Mobley wrote:
David,
I'm using 3.3/3.3.1.
Is there an easy tweak to the source code that would allow something
like this? i.e. could I somehow easily tweak the bit where it reads
the nonbond_params section so I can use an alternate combination rule
there by specifying, say, a different no
David,
I'm using 3.3/3.3.1.
Is there an easy tweak to the source code that would allow something
like this? i.e. could I somehow easily tweak the bit where it reads
the nonbond_params section so I can use an alternate combination rule
there by specifying, say, a different nonbonded parameter typ
Ryogo Sugitani wrote:
2007/4/5, David van der Spoel <[EMAIL PROTECTED]>:
Ryogo Sugitani wrote:
> David,
>
> How about adding [ nonbond_params ] in your ff???nb.itp file
> as shown in p.88 of the user's manual?
> I believe it will override the default vdw interaction for that
> particular atom-ty
2007/4/5, David van der Spoel <[EMAIL PROTECTED]>:
Ryogo Sugitani wrote:
> David,
>
> How about adding [ nonbond_params ] in your ff???nb.itp file
> as shown in p.88 of the user's manual?
> I believe it will override the default vdw interaction for that
> particular atom-type pair.
> (Assuming yo
Ryogo Sugitani wrote:
David,
How about adding [ nonbond_params ] in your ff???nb.itp file
as shown in p.88 of the user's manual?
I believe it will override the default vdw interaction for that
particular atom-type pair.
(Assuming you want to use combination rule #1 just for that atom-type pair)
David,
How about adding [ nonbond_params ] in your ff???nb.itp file
as shown in p.88 of the user's manual?
I believe it will override the default vdw interaction for that
particular atom-type pair.
(Assuming you want to use combination rule #1 just for that atom-type pair)
If I miss your point,
Gromacs users,
I'm using a force field (the port of AMBER to GROMACS) which uses
combination rules (combination rule 2), etc. in terms of sigma and
epsilon. However, I need to be able to modify C6 directly (in
particular, I want to be able to set it to zero). Can anyone give me
any pointers on a
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