On 1/10/13 11:14 AM, Ignacio Fernández Galván wrote:
Dear Gromacs users:
Am I right assuming that [exclusions] do not affect the interactions defined by
[pairs]?
This seems to be implied from the note in section 5.3.4 in the manual: "Note that
one should add exclusions for all atom pairs pa
Dear Gromacs users:
Am I right assuming that [exclusions] do not affect the interactions defined by
[pairs]?
This seems to be implied from the note in section 5.3.4 in the manual: "Note
that one should add exclusions for all atom pairs participating in pair
interactions type 3, otherwise such
Hi all,
In the OPLS-AA tip4p.itp file I see:
[ moleculetype ]
; molname nrexcl
SOL 2
and
[ exclusions ]
1 2 3 4
2 1 3 4
3 1 2 4
4 1 2 3
If bonded interactions are included (FLEXIBLE define
On 12/05/2011 2:43 AM, Gavin Melaugh wrote:
Regarding my earlier post- If someone could confirm.
Taking into account that atom indices start from zero.
Then excls[0] = exclusions centred around atom 1.
[0..12] = there are 13 exclusions each one labelled form 0-12.
I then assume that you read the
Regarding my earlier post- If someone could confirm.
Taking into account that atom indices start from zero.
Then excls[0] = exclusions centred around atom 1.
[0..12] = there are 13 exclusions each one labelled form 0-12.
I then assume that you read the exclusions with respect to atom 0
(actual inde
Hi all
I am cheking the non binary version topol.tpr form grompp and I was
wondering what the following format for the exclusion section signifies?
excls:
nr=228
nra=1920
excls[0][0..12]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16}
excls[1][13..25]={0, 1, 2, 3, 4
On 17/03/2010 9:20 PM, Cristiano De Michele wrote:
Dear GROMACS users,
I created a custom topology file to
define a molecule composed of 5 sites.
Two sites are real massive sites (but for them
C6=C12=0 and their charge is 0, hence they do not interact
with sites of same type on other molecules),
Dear GROMACS users,
I created a custom topology file to
define a molecule composed of 5 sites.
Two sites are real massive sites (but for them
C6=C12=0 and their charge is 0, hence they do not interact
with sites of same type on other molecules),
while remaining three sites are virtual sites.
Two o
so it seems that I don't need to use
exclusions anymore.
Regards,
Reza Salari
From: Berk Hess
To: Discussion list for GROMACS users
Sent: Fri, December 4, 2009 8:01:34 AM
Subject: RE: [gmx-users] Exclusions in topology file seem not working for big
sy
not.
Berk
Date: Thu, 3 Dec 2009 10:40:08 -0800
From: resa...@yahoo.com
Subject: Re: [gmx-users] Exclusions in topology file seem not working for big
systems
To: gmx-users@gromacs.org
Thank you very much Dr Hess.
Then I guess I have to test my rerun workaround that I mentioned for my system.
, 2009 12:06:53 PM
Subject: RE: [gmx-users] Exclusions in topology file seem not working for big
systems
Hi,
I think that for your problem the couple option is not useful.
It does exactly the opposite. I removes all interactions of the selected
molecule type with the rest of the system
and
ns.
(which end up in special 1-4 energy terms).
Berk
Date: Thu, 3 Dec 2009 08:59:12 -0800
From: resa...@yahoo.com
Subject: Re: [gmx-users] Exclusions in topology file seem not working for big
systems
To: gmx-users@gromacs.org
Thanks Dr Hess.
I didn't get an error message when using gromp
3, 2009 3:30:27 AM
Subject: RE: [gmx-users] Exclusions in topology file seem not working for big
systems
Hi,
If you really had too many exclusions you would get an error message.
So I just tested this.
I used the couple_moltype option to couple a 389 atom protein.
This generates exclusions betwe
special 1-4's because
of the couple option).
So I don't understand what is going wrong in your case.
Berk
Date: Wed, 2 Dec 2009 09:31:03 -0800
From: resa...@yahoo.com
Subject: Re: [gmx-users] Exclusions in topology file seem not working for big
systems
To: gmx-users@gromacs.org
Thank
.
Regards,
Reza Salari
From: David van der Spoel
To: Discussion list for GROMACS users
Sent: Wed, December 2, 2009 11:59:49 AM
Subject: Re: [gmx-users] Exclusions in topology file seem not working for big
systems
Reza Salari wrote:
> Hi All,
>
> I seem
Reza Salari wrote:
Hi All,
I seem to have a hard time to use exclusions in topology file. I have a
relatively big system (~400 aa) that I am trying to calculate the
difference in desolvation energy (dA) upon turning off charges on a
specific residue using thermodynamics integration method. Th
Hi All,
I seem to have a hard time to use exclusions in topology file. I have a
relatively big system (~400 aa) that I am trying to calculate the difference in
desolvation energy (dA) upon turning off charges on a specific residue using
thermodynamics integration method. The system is a complex
한상화 wrote:
Hi,
In .rtp file of a GROMOS 96 force field (ffG43a1.rtp for example),
exclusions seem to be listed only for aromatic residues such as TYR,
HIS, and TRP.
Why is that so?
normally they are generated (chapter 4) but one can define extra
exclusions. interactions within rings usualy
Hi,
In .rtp file of a GROMOS 96 force field (ffG43a1.rtp for example),
exclusions seem to be listed only for aromatic residues such as TYR, HIS,
and TRP.
Why is that so?
Sanghwa Han
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