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> Subject: Re: [gmx-users] cgnr in top file
>
>
>
> Erik Marklund wrote:
> > True. I guess gromacs groups together the terminal hydrogens, overriding
> > the original force field parameters. Can't say why that decision was
> > made, but it will infl
Erik Marklund wrote:
True. I guess gromacs groups together the terminal hydrogens, overriding
the original force field parameters. Can't say why that decision was
made, but it will influence your simulation very little.
I think there was a bug report some time ago involving virtual sites on
True. I guess gromacs groups together the terminal hydrogens, overriding
the original force field parameters. Can't say why that decision was
made, but it will influence your simulation very little.
Erik
leila karami skrev:
Dear Erik
you said Amber03 was not parameterized with charge groups
Dear Erik
you said Amber03 was not parameterized with charge groups and last column in
your rtp entry holds the chargegroup numbers. but
cgnr column in my top file does not looks just like it. in case of H1, H2
and H3.
* H1amber99_17 0.16420 2
** H2amber99_17 0.16420 3
leila karami wrote:
Dear Erik
thank for your answer.
my rtp file for amber 03 force field is as follow :
[ NGLY ]
[ atoms ]
Namber99_39 0.29430 1
H1amber99_17 0.16420 2
H2amber99_17 0.16420
The last column in your rtp entry holds the chargegroup numbers. The
cgnr column in your top file looks just like it. Amber03 was not
parameterized with charge groups, so the atoms are not groupt together
as you can see.
Erik
leila karami skrev:
Dear Erik
thank for your answer.
my rtp fi
Dear Erik
thank for your answer.
my rtp file for amber 03 force field is as follow :
[ NGLY ]
[ atoms ]
Namber99_39 0.29430 1
H1amber99_17 0.16420 2
H2amber99_17 0.16420 3
H3amber99_17 0.16420 4
CAamber99_11 -0.01000 5
HA1
Erik Marklund skrev:
leila karami skrev:
Hi all
how cgnr is determind in *.top file? based on?
Any help will highly appreciated!
Depends on the force field. Generally, they're set according to the
chargegroups in the original force field, if the force field was
parameterized with charge
leila karami skrev:
Hi all
how cgnr is determind in *.top file? based on?
Any help will highly appreciated!
Depends on the force field. Generally, they're set according to the
chargegroups in the original force field, if the force field was
parameterized with charge groups, that is.
--
Hi all
how cgnr is determind in *.top file? based on?
Any help will highly appreciated!
--
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rs@gromacs.org
> Subject: [gmx-users] cgnr
>
> Hi
> As Justin described,
> cgnr = charge group number
>
> could anyone explain more about this ?
> and, how to determin cgnr?
>
> Thanks
> Lin
> ___
> gmx-users mailing
Hi
As Justin described,
cgnr = charge group number
could anyone explain more about this ?
and, how to determin cgnr?
Thanks
Lin
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wangcl wrote:
Hi,
In manual gmx 3.3, I find “if possible, the total charge of a charge
group should be zero” .
In my systems, I want to do an artificial charge distribution model. So
I have some questions:
1. I don’t know whether it is right that I don’t make the total
charge to z
Hi,
In manual gmx 3.3, I find "if possible, the total charge of a charge
group should be zero" .
In my systems, I want to do an artificial charge distribution model. So I
have some questions:
1. I don't know whether it is right that I don't make the total charge
to zero in one charge gro
Stephanie Bluebear wrote:
Dear Simulators,
Do the numbers in the cgnr column necessarily need to be in ascending
order? I have a topology of a molecule and would like to acetylate some
residues, whose atoms numbers (and charge group numbers) are in the
middle of the pack . I have added the at
Stephanie Bluebear wrote:
Dear Simulators,
Do the numbers in the cgnr column necessarily need to be in ascending
order? I have a topology of a molecule and would like to acetylate some
residues, whose atoms numbers (and charge group numbers) are in the
middle of the pack . I have added the at
Dear Simulators, Do the numbers in the cgnr column necessarily need to be in ascending order? I have a topology of a molecule and would like to acetylate some residues, whose atoms numbers (and charge group numbers) are in the middle of the pack . I have added the atoms I need to add at the end of
davood ajloo wrote:
I want to construct the trp file for a nanotube, I used prodrg but it
could not calculate for non flat sp2 carbon(nanotube) . I used X2top to
creating the top file from pdb (from Hyperchm), It only gave me the
connetction, no bond and angles and others parameters. I got the
I want to construct the trp file for a nanotube, I used prodrg but it could not calculate for non flat sp2 carbon(nanotube) . I used X2top to creating the top file from pdb (from Hyperchm), It only gave me the connetction, no bond and angles and others parameters. I got them from literature and pu
davood ajloo wrote:
Dear gmx-users
I want to classifying the charge on the basis of cgnr charge type. How I
do it?
please explain better what you want to do.
Thanks a lot of
Ajloo
__
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Dear gmx-users I want to classifying the charge on the basis of cgnr charge type. How I do it? Thanks a lot of Ajloo __Do You Yahoo!?Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _
Thank you!
Please disregard my last comment in bugzilla.
Marcelo.
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Berk Hess
Sent: Friday, May 05, 2006 8:48 AM
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] cgnr
I have fixed the bug.
You can avoid
I have fixed the bug.
You can avoid the bug in the 3.3.1 release by setting the environment
variable:
GMX_NO_SOLV_OPT
Berk.
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From: "Marcelo A. Carignano" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: "'Discussion list for GROMACS users'"
Subject: RE: [gmx-users] cgnr
Date: Thu, 4 May 2006 16:35:29 -0400
Done. Posted bug # 75.
I hope my explanation is cle
Done. Posted bug # 75.
I hope my explanation is clear.
Marcelo.
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of David van der Spoel
Sent: Thursday, May 04, 2006 4:05 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] cgnr
Marcelo A
David van der Spoel
Sent: Thursday, May 04, 2006 3:21 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] cgnr
Marcelo A. Carignano wrote:
Thank you David, but there is no such a term in this case:
I see, make the cut-off larger. mdrun uses charge group based cutoff
(see chap 4
list for GROMACS users
Subject: Re: [gmx-users] cgnr
Marcelo A. Carignano wrote:
> Thank you David, but there is no such a term in this case:
>
I see, make the cut-off larger. mdrun uses charge group based cutoff
(see chap 4) and you are probably missing some interactions in the
secon
Marcelo A. Carignano wrote:
Thank you David, but there is no such a term in this case:
I see, make the cut-off larger. mdrun uses charge group based cutoff
(see chap 4) and you are probably missing some interactions in the
second case.
$g_energy
(deleted lines)
Select the t
Thank you David, but there is no such a term in this case:
$g_energy
(deleted lines)
Select the terms you want from the following list
-
LJ-(SR)Coulomb-(SR) Potential Kinetic-En.Total-Energy
TemperaturePre
Marcelo A. Carignano wrote:
Dear all:
I'm running a test case defining all the interaction parameters in the
topol.top file. My system consist of two NH3 molecules.
Every thing goes well except for the role played by the "cgnr" values:
Depending on how I assign these numbers the calculated Coulo
Dear all:
I'm running a test case defining all the interaction parameters in the
topol.top file. My system consist of two NH3 molecules.
Every thing goes well except for the role played by the "cgnr" values:
Depending on how I assign these numbers the calculated Coulombic
interaction changes. If I
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